From 9a1c0c4758cb07db5d4485f132d590c58b709279 Mon Sep 17 00:00:00 2001
From: kartikeyakirar <kartikeyakirar@users.noreply.github.com>
Date: Fri, 13 Oct 2023 09:53:37 +0000
Subject: [PATCH] deploy: d71a227f983a27d8b9e50f89a7d2e1c1e0a7d73f

---
 main/coverage-report/index.html | 25792 +++++++++++++++---------------
 1 file changed, 12952 insertions(+), 12840 deletions(-)

diff --git a/main/coverage-report/index.html b/main/coverage-report/index.html
index c0864abd..f2812e8a 100644
--- a/main/coverage-report/index.html
+++ b/main/coverage-report/index.html
@@ -94,7 +94,7 @@
   font-size: 11px;
 }</style>
   <div class="col-md-8 col-md-offset-2">
-    <h2>teal.modules.hermes coverage - 26.54%</h2>
+    <h2>teal.modules.hermes coverage - 26.38%</h2>
     <div class="tabbable">
       <ul class="nav nav-tabs" data-tabsetid="covr">
         <li class="active">
@@ -106,19 +106,19 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
       </ul>
       <div class="tab-content" data-tabsetid="covr">
         <div class="tab-pane active" title="Files" data-value="Files" id="tab-covr-1">
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+          <script type="application/json" data-for="htmlwidget-77bcc2a9d07b5ab99e9f">{"x":{"filter":"none","vertical":false,"fillContainer":false,"data":[["<a href=\"#\">R/zzz.R<\/a>","<a href=\"#\">R/forestplot.R<\/a>","<a href=\"#\">R/volcanoplot.R<\/a>","<a href=\"#\">R/boxplot.R<\/a>","<a href=\"#\">R/km.R<\/a>","<a href=\"#\">R/scatterplot.R<\/a>","<a href=\"#\">R/barplot.R<\/a>","<a href=\"#\">R/pca.R<\/a>","<a href=\"#\">R/quality.R<\/a>","<a href=\"#\">R/assaySpec.R<\/a>","<a href=\"#\">R/adtteSpec.R<\/a>","<a href=\"#\">R/experimentSpec.R<\/a>","<a href=\"#\">R/geneSpec.R<\/a>","<a href=\"#\">R/sampleVarSpec.R<\/a>","<a href=\"#\">R/checkmate.R<\/a>","<a href=\"#\">R/utils.R<\/a>"],[3,315,283,263,310,261,262,467,434,152,398,283,483,524,140,79],[1,166,157,148,160,143,142,289,246,40,133,73,202,183,17,14],[0,21,25,24,26,25,27,66,58,11,40,29,85,90,9,14],[1,145,132,124,134,118,115,223,188,29,93,44,117,93,8,0],["0","0","0","0","0","0","0","0","0","2","2","2","3","1","4","8"],["0.00%","12.65%","15.92%","16.22%","16.25%","17.48%","19.01%","22.84%","23.58%","27.50%","30.08%","39.73%","42.08%","49.18%","52.94%","100.00%"]],"container":"<table class=\"row-border\">\n  <thead>\n    <tr>\n      <th>File<\/th>\n      <th>Lines<\/th>\n      <th>Relevant<\/th>\n      <th>Covered<\/th>\n      <th>Missed<\/th>\n      <th>Hits / Line<\/th>\n      <th>Coverage<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"searching":false,"dom":"t","paging":false,"columnDefs":[{"targets":6,"createdCell":"function(td, cellData, rowData, row, col) {\n  var percent = cellData.replace(\"%\", \"\");\n  if (percent > 90) {\n    var grad = \"linear-gradient(90deg, #edfde7 \" + cellData + \", white \" + cellData + \")\";\n  } else if (percent > 75) {\n    var grad = \"linear-gradient(90deg, #f9ffe5 \" + cellData + \", white \" + cellData + \")\";\n  } else {\n    var grad = \"linear-gradient(90deg, #fcece9 \" + cellData + \", white \" + cellData + \")\";\n  }\n  $(td).css(\"background\", grad);\n}\n"},{"className":"dt-right","targets":[1,2,3,4]}],"order":[],"autoWidth":false,"orderClasses":false},"callback":"function(table) {\ntable.on('click.dt', 'a', function() {\n  files = $('div#files div');\n  files.not('div.hidden').addClass('hidden');\n  id = $(this).text();\n  files.filter('div[id=\\'' + id + '\\']').removeClass('hidden');\n  $('ul.nav a[data-value=Source]').text(id).tab('show');\n});\n}","selection":{"mode":"multiple","selected":null,"target":"row","selectable":null}},"evals":["options.columnDefs.0.createdCell","callback"],"jsHooks":[]}</script>
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         <div class="tab-pane" title="Source" data-value="Source" id="tab-covr-2">
           <div id="files">
-            <div id="R/volcanoplot.R" class="hidden">
+            <div id="R/experimentSpec.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for RNA-seq Volcano Plot</pre>
+                      <pre class="language-r">#' Module Input for Experiment Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -146,28 +146,28 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This module provides an interactive volcano plot for RNA-seq gene expression</pre>
+                      <pre class="language-r">#' This defines the input for the experiment specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' analysis.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#' @param label_experiments (`string`)\cr label for the experiment selection.</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -181,14 +181,14 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">#' @return The UI part.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @seealso [experimentSpecServer()] for the module server and a complete example.</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -202,1881 +202,1895 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">experimentSpecInput &lt;- function(inputId, # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">                                data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">                                mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">                                label_experiments = "Select Experiment") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">17</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">  assert_string(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">18</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r">  assert_string(mae_name, min.chars = 1L)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">19</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">  assert_string(label_experiments, min.chars = 1L)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">20</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules(</pre>
+                      <pre class="language-r">  mae &lt;- data[[mae_name]]()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">21</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     tm_g_volcanoplot(</pre>
+                      <pre class="language-r">  name_choices &lt;- names(mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       label = "volcanoplot",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">23</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">24</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">  selectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">25</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">    inputId = ns("name"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">26</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">    label = label_experiments,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">27</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">    choices = name_choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_volcanoplot &lt;- function(label,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             mae_name,</pre>
+                      <pre class="language-r">#' Helper Function to Order Gene Choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             exclude_assays = character(),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             pre_output = NULL,</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             post_output = NULL) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">35</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  logger::log_info("Initializing tm_g_volcanoplot")</pre>
+                      <pre class="language-r">#' The possible gene choices are ordered as follows. First come all genes which</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">36</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">#' have a non-empty name, ordered by their name alphabetically. Last come</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">37</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">#' all genes with an empty name, ordered by their ID alphabetically.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">38</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">39</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">#' @param genes (`data.frame`)\cr containing `id` and `name` columns of the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">40</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">#'   gene choices. Note that no missing values are allowed.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">42</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
+                      <pre class="language-r">#' @return The ordered `data.frame`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">43</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">44</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_volcanoplot,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">45</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">46</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">#' genes &lt;- data.frame(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">47</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">#'   id = c("7", "1", "2", "345346", "0"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">#'   name = c("e", "", "c", "", "a")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">49</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_volcanoplot,</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">50</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">#' h_order_genes(genes)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">51</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">h_order_genes &lt;- function(genes) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">52</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">  assert_data_frame(genes, types = "character", any.missing = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">53</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">  assert_set_equal(names(genes), c("id", "name"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">55</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = mae_name</pre>
+                      <pre class="language-r">  has_empty_name &lt;- genes$name == ""</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">56</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  first_genes &lt;- which(!has_empty_name)[order(genes[!has_empty_name, ]$name)]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">57</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  last_genes &lt;- which(has_empty_name)[order(genes[has_empty_name, ]$id)]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">58</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  genes[c(first_genes, last_genes), ]</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_volcanoplot sets up the user interface.</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' Helper Function to Format Gene Choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ui_g_volcanoplot &lt;- function(id,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             data,</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             mae_name,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             pre_output,</pre>
+                      <pre class="language-r">#' Given a [`hermes::AnyHermesData`] data object, as well as the annotation</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             post_output) {</pre>
+                      <pre class="language-r">#' column name to use as gene name, this function formats the contained genes</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">67</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">#' as a `data.frame` ready for consumption in [h_order_genes()] e.g.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">68</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- data[[mae_name]]</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @details</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">70</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">#' Note that missing names or names that only contain whitespace</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">71</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output = div(</pre>
+                      <pre class="language-r">#' are replaced by empty strings for consistency and better labeling in the</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">72</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                      <pre class="language-r">#' UI downstream</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">73</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      DT::DTOutput(ns("table"))</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">#' @inheritParams function_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">75</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pre_output = pre_output,</pre>
+                      <pre class="language-r">#' @inheritParams experimentSpecServer</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">76</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    post_output = post_output,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">77</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    encoding = div(</pre>
+                      <pre class="language-r">#' @return A `data.frame` with `id` and `name` columns containing all genes from</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ### Reporter</pre>
+                      <pre class="language-r">#'   `object`.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">79</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">80</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ###</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">81</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">82</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r">#' object &lt;- hermes::hermes_data[1:10, ]</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">83</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r">#' h_gene_data(object, "symbol")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">84</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r">h_gene_data &lt;- function(object, name_annotation) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">85</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sampleVarSpecInput(ns("compare_group"), "Compare Groups", "Please group here into 2 levels"),</pre>
+                      <pre class="language-r">  assert_true(hermes::is_hermes_data(object))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">86</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Show Top Differentiated Genes"),</pre>
+                      <pre class="language-r">  assert_string(name_annotation, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">87</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      shinyWidgets::switchInput(ns("show_top_gene"), value = FALSE, size = "mini"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">88</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::panel_group(</pre>
+                      <pre class="language-r">  gene_ids &lt;- hermes::genes(object)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">89</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::panel_item(</pre>
+                      <pre class="language-r">  gene_names &lt;- if (!is.null(name_annotation)) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">90</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input_id = "settings_item",</pre>
+                      <pre class="language-r">    annotation_data &lt;- hermes::annotation(object)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">91</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          collapsed = TRUE,</pre>
+                      <pre class="language-r">    assert_subset(name_annotation, names(annotation_data))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">92</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = "Additional Settings",</pre>
+                      <pre class="language-r">    annotation_vector &lt;- annotation_data[[name_annotation]]</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">93</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selectInput(ns("method"), "Method", choices = c("voom", "deseq2")),</pre>
+                      <pre class="language-r">    annotation_missing &lt;- is.na(annotation_vector) | grepl("^\\s+$", annotation_vector)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">94</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sliderInput(ns("log2_fc_thresh"), "Log2 fold change threshold", value = 2.5, min = 0.1, max = 10),</pre>
+                      <pre class="language-r">    annotation_vector[annotation_missing] &lt;- ""</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">95</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sliderInput(ns("adj_p_val_thresh"), "Adjusted p-value threshold", value = 0.05, min = 0.001, max = 1)</pre>
+                      <pre class="language-r">    annotation_vector</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">96</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">  } else {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    ""</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">99</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  data.frame(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">100</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    id = gene_ids,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">101</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    name = gene_names</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_volcanoplot sets up the server with reactive graph.</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_volcanoplot &lt;- function(id,</pre>
+                      <pre class="language-r">#' Module Server for Experiment Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              data,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              filter_panel_api,</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              reporter,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              mae_name,</pre>
+                      <pre class="language-r">#' This defines the server part for the experiment specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">110</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              exclude_assays) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">111</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">112</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">#' @param name_annotation (`string` or `NULL`)\cr which annotation column to use as name</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">113</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">#'   to return in the `genes` data. If `NULL`, then the `name` column will be set to empty</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   strings.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">115</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">#' @param sample_vars_as_factors (`flag`)\cr whether to convert the sample variables</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">116</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment_data &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">#'   (columns in `colData()` of the experiment) from character to factor variables.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">117</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">#' @param with_mae_col_data (`flag`)\cr whether to include the `colData()` of the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">118</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">#'   MAE into the experiment `colData()`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">119</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name</pre>
+                      <pre class="language-r">#' @return List with the following reactive objects:</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'   - `data`: the [`hermes::AnyHermesData`] experiment.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">121</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">#'   - `name`: the name of the experiment as selected by the user.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">122</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r">#'   - `genes`: a `data.frame` with the genes in `data`, with columns `id` and `name`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">123</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = experiment_data$assays,</pre>
+                      <pre class="language-r">#'   - `assays`: the names of the assays in `data`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">124</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">125</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' @seealso [experimentSpecInput()] for the module UI.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">126</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    compare_group &lt;- sampleVarSpecServer(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">127</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "compare_group",</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">128</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment_data$name,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">129</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = experiment_data$data,</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">130</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      num_levels = 2L,</pre>
+                      <pre class="language-r">#' ui &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">131</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      label_modal_title = "Please click to group into exactly 2 levels, first level is reference"</pre>
+                      <pre class="language-r">#'                data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'                mae_name) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the filtered data set or the chosen experiment changes, update</pre>
+                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # the differential expression results.</pre>
+                      <pre class="language-r">#'     encoding = div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">136</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    diff_expr &lt;- reactive({</pre>
+                      <pre class="language-r">#'       experimentSpecInput(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">137</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      object &lt;- compare_group$experiment_data()</pre>
+                      <pre class="language-r">#'         ns("my_experiment"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">138</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      compare_group &lt;- compare_group$sample_var()</pre>
+                      <pre class="language-r">#'         data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">139</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      method &lt;- input$method</pre>
+                      <pre class="language-r">#'         mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'         label_experiments = "Please choose experiment"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">141</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">#'       ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">142</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object,</pre>
+                      <pre class="language-r">#'       selectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">143</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        method</pre>
+                      <pre class="language-r">#'         ns("property"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'         "Please choose property",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">145</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">#'         c("data", "name", "genes", "assays")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">146</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        !is.null(compare_group),</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">147</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Please select a group variable"</pre>
+                      <pre class="language-r">#'     ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">148</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">#'     output = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">149</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'       verbatimTextOutput(ns("summary")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">150</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::diff_expression(</pre>
+                      <pre class="language-r">#'       verbatimTextOutput(ns("head"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">151</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object,</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">152</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        group = compare_group,</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">153</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        method = method</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">154</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' server &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'                    data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">157</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
+                      <pre class="language-r">#'                    filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">158</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      diff_expr_result &lt;- diff_expr()</pre>
+                      <pre class="language-r">#'                    mae_name) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">159</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      log2_fc_thresh &lt;- input$log2_fc_thresh</pre>
+                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">160</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adj_p_val_thresh &lt;- input$adj_p_val_thresh</pre>
+                      <pre class="language-r">#'     experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'       "my_experiment",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">162</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">#'       data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">163</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        log2_fc_thresh,</pre>
+                      <pre class="language-r">#'       filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">164</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        adj_p_val_thresh</pre>
+                      <pre class="language-r">#'       mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">165</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'     result &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">167</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::autoplot(</pre>
+                      <pre class="language-r">#'       switch(input$property,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">168</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        diff_expr_result,</pre>
+                      <pre class="language-r">#'         data = experiment$data(),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">169</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        adj_p_val_thresh = adj_p_val_thresh,</pre>
+                      <pre class="language-r">#'         name = experiment$name(),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">170</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        log2_fc_thresh = log2_fc_thresh</pre>
+                      <pre class="language-r">#'         genes = experiment$genes(),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'         assays = experiment$assays()</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">173</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'     output$summary &lt;- renderPrint({</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">175</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws_p &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">#'       result &lt;- result()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">176</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot",</pre>
+                      <pre class="language-r">#'       hermes::summary(result)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">177</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = plot_r</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'     output$head &lt;- renderPrint({</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">179</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'       result &lt;- result()</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Display top genes if switched on.</pre>
+                      <pre class="language-r">#'       utils::head(result)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">181</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    show_top_gene_diffexpr &lt;- reactive({</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">182</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (input$show_top_gene) {</pre>
+                      <pre class="language-r">#'   })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">183</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        result &lt;- diff_expr()</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">184</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        with(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">185</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          result,</pre>
+                      <pre class="language-r">#' my_app &lt;- function() {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">186</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          data.frame(</pre>
+                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">187</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            log2_fc = round(log2_fc, 2),</pre>
+                      <pre class="language-r">#'   mae_name &lt;- "MAE"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">188</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            stat = round(stat, 2),</pre>
+                      <pre class="language-r">#'   mae_data &lt;- dataset(mae_name, mae)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">189</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            p_val = format.pval(p_val),</pre>
+                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">190</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            adj_p_val = format.pval(adj_p_val),</pre>
+                      <pre class="language-r">#'   app &lt;- init(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">191</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            row.names = rownames(result)</pre>
+                      <pre class="language-r">#'     data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">192</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">#'     modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">193</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'       module(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">#'         label = "experimentSpec example",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">195</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        NULL</pre>
+                      <pre class="language-r">#'         server = server,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">196</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'         server_args = list(mae_name = mae_name),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'         ui = ui,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'         ui_args = list(mae_name = mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">199</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$table &lt;- DT::renderDT({</pre>
+                      <pre class="language-r">#'         datanames = "all"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">200</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      DT::datatable(</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">201</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_top_gene_diffexpr(),</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">202</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        rownames = TRUE,</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">203</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        options = list(scrollX = TRUE, pageLength = 30, lengthMenu = c(5, 15, 30, 100)),</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">204</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        caption = "Top Differentiated Genes"</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'   my_app()</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">207</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">208</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
+                      <pre class="language-r">experimentSpecServer &lt;- function(id, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">209</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">                                 data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">210</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">                                 filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">211</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">                                 mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">212</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Volcano Plot")</pre>
+                      <pre class="language-r">                                 name_annotation = "symbol",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">213</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Volcano Plot", "header2")</pre>
+                      <pre class="language-r">                                 sample_vars_as_factors = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">214</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">                                 with_mae_col_data = TRUE) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">215</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r">  assert_string(id)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">216</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">217</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Experiment:",</pre>
+                      <pre class="language-r">  assert_string(mae_name, min.chars = 1L)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">218</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`experiment-name`,</pre>
+                      <pre class="language-r">  assert_string(name_annotation, min.chars = 1L, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">219</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAssay:",</pre>
+                      <pre class="language-r">  assert_flag(sample_vars_as_factors)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">220</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`assay-name`,</pre>
+                      <pre class="language-r">  assert_flag(with_mae_col_data)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">221</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nCompare Groups:",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">222</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`compare_group-sample_var`,</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">223</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nShow Top Differentiated Genes:",</pre>
+                      <pre class="language-r">    # When the filtered data set of the chosen experiment changes, update the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">224</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$show_top_gene,</pre>
+                      <pre class="language-r">    # experiment data object.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">225</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nMethod:",</pre>
+                      <pre class="language-r">    data_return &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">226</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$method,</pre>
+                      <pre class="language-r">      name &lt;- input$name</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">227</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nLog2fold Change Threshold:",</pre>
+                      <pre class="language-r">      req(name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">228</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$log2_fc_thresh,</pre>
+                      <pre class="language-r">      mae &lt;- data[[mae_name]]()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">229</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAdjusted P-value Threshold:",</pre>
+                      <pre class="language-r">      orig_object &lt;- mae[[name]]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">230</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$adj_p_val_thresh</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">231</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">        hermes::is_hermes_data(orig_object),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">232</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">        "Please first convert your experiment to HermesData class"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">233</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">234</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">235</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">        !hermes::isEmpty(orig_object),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">236</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">        "No genes or samples included in this experiment, please adjust filters"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">237</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">238</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">      object &lt;- if (with_mae_col_data) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">239</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        MultiAssayExperiment::getWithColData(mae, name)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">240</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">241</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">        orig_object</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">242</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws_p$dim())</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">243</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (isTRUE(input$show_top_gene)) {</pre>
+                      <pre class="language-r">      if (sample_vars_as_factors) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">244</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Table", "header3")</pre>
+                      <pre class="language-r">        SummarizedExperiment::colData(object) &lt;-</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">245</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_table(show_top_gene_diffexpr())</pre>
+                      <pre class="language-r">          hermes::df_cols_to_factor(SummarizedExperiment::colData(object))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">246</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">247</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">      object</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">248</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">249</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">250</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">    # When the filtered data set or the chosen experiment changes, update</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">251</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
+                      <pre class="language-r">    # the calls that subset the genes of the chosen experiment data object.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">252</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">    subset_calls &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">253</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
+                      <pre class="language-r">      name &lt;- input$name</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">254</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">      req(name)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">255</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">256</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">      filter_states &lt;- filter_panel_api$get_filter_state()[[mae_name]][[name]]["subset"]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">257</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      filter_states</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">258</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">259</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_volcanoplot sample module function.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">260</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">    # Only when the chosen gene subset changes, we recompute gene choices</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">261</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">    genes &lt;- eventReactive(subset_calls(), ignoreNULL = FALSE, {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">262</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      data_return &lt;- data_return()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">263</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r">      genes &lt;- h_gene_data(data_return, name_annotation)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">264</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">      h_order_genes(genes)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">265</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_volcanoplot()</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">266</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">267</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_volcanoplot &lt;- function() {</pre>
+                      <pre class="language-r">    # When the chosen experiment changes, recompute the assay names.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">268</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">    assays &lt;- eventReactive(input$name, ignoreNULL = TRUE, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">269</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">      data_return &lt;- data_return()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">270</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
+                      <pre class="language-r">      SummarizedExperiment::assayNames(data_return)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">271</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">272</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">273</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = teal::modules(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">274</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tm_g_volcanoplot(</pre>
+                      <pre class="language-r">    list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">275</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = "volcanoplot",</pre>
+                      <pre class="language-r">      data = data_return,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">276</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae_name = "MAE"</pre>
+                      <pre class="language-r">      name = reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">277</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">        input$name</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">278</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      }), # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">279</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      genes = genes,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">280</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">      assays = assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">281</td>
                     <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">282</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  })</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">283</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
@@ -2084,14 +2098,14 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                 </tbody>
               </table>
             </div>
-            <div id="R/adtteSpec.R" class="hidden">
+            <div id="R/boxplot.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Data Preprocessing for `ADTTE` Module</pre>
+                      <pre class="language-r">#' Teal Module for RNA-seq Boxplot</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -2119,56 +2133,56 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' A function to help with merging of MAE to `ADTTE`.</pre>
+                      <pre class="language-r">#' This module provides an interactive boxplot for RNA-seq gene expression</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' analysis.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams function_arguments</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return A data frame containing all columns/rows from `adtte` that match</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   by subject ID with the row names of the MAE and have the gene samples available</pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   in the given experiment. The attribute `gene_cols` contains the column names</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   for the gene columns.</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -2182,22222 +2196,22298 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @note The final gene column names can start with a different string than</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   the original gene IDs (or labels), in particular white space and colons are removed.</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">#'   modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dplyr::mutate(CNSR = as.logical(CNSR))</pre>
+                      <pre class="language-r">#'     tm_g_boxplot(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       label = "boxplot",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' new_adtte &lt;- h_km_mae_to_adtte(</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   adtte,</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae,</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   genes = hermes::gene_spec("GeneID:1820"),</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   experiment_name = "hd2"</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' new_adtte2 &lt;- h_km_mae_to_adtte(</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   adtte,</pre>
+                      <pre class="language-r">tm_g_boxplot &lt;- function(label,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae,</pre>
+                      <pre class="language-r">                         mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   genes = hermes::gene_spec(c("GeneID:1820", "GeneID:94115"), fun = colMeans),</pre>
+                      <pre class="language-r">                         exclude_assays = character(),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   experiment_name = "hd2"</pre>
+                      <pre class="language-r">                         summary_funs = list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">                           None = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' new_adtte3 &lt;- h_km_mae_to_adtte(</pre>
+                      <pre class="language-r">                           Mean = colMeans,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   adtte,</pre>
+                      <pre class="language-r">                           Median = matrixStats::colMedians,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae,</pre>
+                      <pre class="language-r">                           Max = matrixStats::colMaxs</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   genes = hermes::gene_spec(c(A = "GeneID:1820", B = "GeneID:94115")),</pre>
+                      <pre class="language-r">                         ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   experiment_name = "hd2"</pre>
+                      <pre class="language-r">                         pre_output = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">                         post_output = NULL) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">41</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_km_mae_to_adtte &lt;- function(adtte,</pre>
+                      <pre class="language-r">  logger::log_info("Initializing tm_g_boxplot")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">42</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              mae,</pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">43</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              genes,</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">44</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              experiment_name = "hd1",</pre>
+                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">45</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              assay_name = "counts",</pre>
+                      <pre class="language-r">  assert_summary_funs(summary_funs, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">46</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              usubjid_var = "USUBJID") {</pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">47</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(mae, "MultiAssayExperiment")</pre>
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">48</td>
-                    <td class="coverage">11<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(experiment_name)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">49</td>
-                    <td class="coverage">10<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(usubjid_var)</pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">50</td>
-                    <td class="coverage">10<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_names(names(adtte), must.include = usubjid_var)</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">51</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    server = srv_g_boxplot,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">52</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  # Check subject ID across experiment, sample map, and MAE colData.</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">53</td>
-                    <td class="coverage">10<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_samplemap &lt;- MultiAssayExperiment::sampleMap(mae)</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">54</td>
-                    <td class="coverage">10<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  samplemap_experiment &lt;- mae_samplemap[mae_samplemap$assay == experiment_name, ]</pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">55</td>
-                    <td class="coverage">10<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  sm_usubjid &lt;- as.character(samplemap_experiment$primary)</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">57</td>
-                    <td class="coverage">10<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hd &lt;- suppressWarnings(MultiAssayExperiment::getWithColData(mae, experiment_name))</pre>
+                      <pre class="language-r">    ui = ui_g_boxplot,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">58</td>
-                    <td class="coverage">9<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(hd, "AnyHermesData")</pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">59</td>
-                    <td class="coverage">9<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hd_usubjid &lt;- as.character(SummarizedExperiment::colData(hd)[[usubjid_var]])</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">60</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">61</td>
-                    <td class="coverage">9<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_subset(</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">62</td>
-                    <td class="coverage">9<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x = hd_usubjid,</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">63</td>
-                    <td class="coverage">9<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    choices = sm_usubjid</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">64</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    datanames = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">66</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_coldata &lt;- MultiAssayExperiment::colData(mae)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">67</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (usubjid_var %in% colnames(mae_coldata)) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">68</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    mae_usubjid &lt;- as.character(mae_coldata[[usubjid_var]])</pre>
+                      <pre class="language-r">#' @describeIn tm_g_boxplot sets up the user interface.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">69</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assert_subset(</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">70</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      x = sm_usubjid,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">71</td>
-                    <td class="coverage">8<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      choices = mae_usubjid</pre>
+                      <pre class="language-r">ui_g_boxplot &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                         data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">                         mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                         summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">75</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  gene_data &lt;- hermes::col_data_with_genes(</pre>
+                      <pre class="language-r">                         pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">76</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    object = hd,</pre>
+                      <pre class="language-r">                         post_output) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">77</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay_name = assay_name,</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">78</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    genes = genes</pre>
+                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">79</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    encoding = div(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">80</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  merged_adtte &lt;- hermes::inner_join_cdisc(</pre>
+                      <pre class="language-r">      ### Reporter</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">81</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    gene_data = gene_data,</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">82</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    cdisc_data = adtte,</pre>
+                      <pre class="language-r">      ###</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">83</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    patient_key = usubjid_var</pre>
+                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">84</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">85</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  structure(</pre>
+                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">86</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    merged_adtte,</pre>
+                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">87</td>
-                    <td class="coverage">5<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    gene_cols = attr(gene_data, "gene_cols")</pre>
+                      <pre class="language-r">      geneSpecInput(ns("genes"), summary_funs),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">88</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      tags$label("Jitter"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">89</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      shinyWidgets::switchInput(ns("jitter"), value = FALSE, size = "mini"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">90</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      tags$label("Violin Plot"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">91</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Input for `ADTTE` Specification</pre>
+                      <pre class="language-r">      shinyWidgets::switchInput(ns("violin"), value = FALSE, size = "mini"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">92</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      teal.widgets::panel_group(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">93</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">        teal.widgets::panel_item(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">94</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          input_id = "settings_item",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">95</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the input for the `ADTTE` specification.</pre>
+                      <pre class="language-r">          collapsed = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">96</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          title = "Additional Settings",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">97</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("strat"), "Optional stratifying variable"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">98</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_paramcd (`string`)\cr label for the endpoint (`PARAMCD`) selection.</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("color"), "Optional color variable"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">99</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("facet"), "Optional facet variable")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The UI part.</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [adtteSpecServer()] for the module server and a complete example.</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">103</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">adtteSpecInput &lt;- function(inputId, # nolint</pre>
+                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">104</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           label_paramcd = "Select Endpoint") {</pre>
+                      <pre class="language-r">    pre_output = pre_output,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">105</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(inputId)</pre>
+                      <pre class="language-r">    post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">106</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_paramcd, min.chars = 1L)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">108</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @describeIn tm_g_boxplot sets up the server with reactive graph.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">110</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tagList(</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">111</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    selectizeInput(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">112</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      inputId = ns("paramcd"),</pre>
+                      <pre class="language-r">srv_g_boxplot &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">113</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      label = label_paramcd,</pre>
+                      <pre class="language-r">                          data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">114</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      choices = "",</pre>
+                      <pre class="language-r">                          filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">115</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      options = list(placeholder = "- Nothing selected -")</pre>
+                      <pre class="language-r">                          reporter,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">                          mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">117</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    include_js_files("dropdown.js")</pre>
+                      <pre class="language-r">                          exclude_assays,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">                          summary_funs) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">119</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">120</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">121</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Server for `ADTTE` Specification</pre>
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">122</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">123</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">124</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">125</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the server part for the `ADTTE` specification. The resulting data</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">126</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' set `binned_adtte_subset` contains the subset of `ADTTE` selected by the time-to-event</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">127</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' endpoint, joined together with the gene information extracted from specified assay</pre>
+                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">128</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' and experiment, as numeric and factor columns. The factor column is created by binning</pre>
+                      <pre class="language-r">      mae_name = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">129</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' the numeric column according to the quantile cutoffs specified in `probs`.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">130</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">131</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">132</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param experiment_data (reactive `AnyHermesData`)\cr input experiment.</pre>
+                      <pre class="language-r">      assays = experiment$assays,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">133</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param experiment_name (reactive `string`)\cr name of the input experiment.</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param assay (reactive `string`)\cr name of the assay.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">135</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param genes (reactive `GeneSpec`)\cr gene specification.</pre>
+                      <pre class="language-r">    multi &lt;- multiSampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">136</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param probs (reactive `numeric`)\cr probabilities to bin the gene or gene signature</pre>
+                      <pre class="language-r">      inputIds = c("strat", "color", "facet"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">137</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   into.</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">138</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      original_data = experiment$data</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return List with the following elements:</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">140</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `binned_adtte_subset`: reactive containing the joined `ADTTE` and gene data.</pre>
+                      <pre class="language-r">    genes &lt;- geneSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">141</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `gene_col`: reactive containing the string with the column name of the original</pre>
+                      <pre class="language-r">      "genes",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">142</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'        numeric gene variable.</pre>
+                      <pre class="language-r">      funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">143</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `gene_factor`: string with the variable name for the binned gene data.</pre>
+                      <pre class="language-r">      gene_choices = experiment$genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `time_unit`: reactive string with the time unit for the current subset.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">145</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [adtteSpecInput()] for the module UI.</pre>
+                      <pre class="language-r">      # Resolve all reactivity.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">147</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      experiment_data &lt;- multi$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">148</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      strat &lt;- multi$vars$strat()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">149</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      genes &lt;- genes()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">150</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      facet &lt;- multi$vars$facet()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">151</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ui &lt;- function(id,</pre>
+                      <pre class="language-r">      color &lt;- multi$vars$color()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">152</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                data) {</pre>
+                      <pre class="language-r">      assay &lt;- assay()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">153</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
+                      <pre class="language-r">      jitter &lt;- input$jitter</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">154</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      violin &lt;- input$violin</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">156</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     encoding = div(</pre>
+                      <pre class="language-r">      req(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">157</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experimentSpecInput(ns("experiment"), data = data, mae_name = "MAE"),</pre>
+                      <pre class="language-r">        assay,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r">        # Note: The following statements are important to make sure the UI inputs have been updated.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">159</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       geneSpecInput(ns("genes"), funs = list(Mean = colMeans)),</pre>
+                      <pre class="language-r">        isTRUE(assay %in% SummarizedExperiment::assayNames(experiment_data)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">160</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       adtteSpecInput(ns("adtte"))</pre>
+                      <pre class="language-r">        is.null(facet) || isTRUE(facet %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">161</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     ),</pre>
+                      <pre class="language-r">        is.null(color) || isTRUE(color %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">162</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output = verbatimTextOutput(ns("summary"))</pre>
+                      <pre class="language-r">        is.null(strat) || isTRUE(strat %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">163</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">        cancelOutput = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">164</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">165</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">166</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' server &lt;- function(id, data, filter_panel_api) {</pre>
+                      <pre class="language-r">      validate_gene_spec(genes, rownames(experiment_data))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">167</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">168</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">      hermes::draw_boxplot(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">169</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "experiment",</pre>
+                      <pre class="language-r">        object = experiment_data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">170</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       data = data,</pre>
+                      <pre class="language-r">        assay_name = assay,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">171</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">        genes = genes,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">172</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">        x_var = strat,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">173</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">        facet_var = facet,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">174</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">        color_var = color,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">175</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "assay",</pre>
+                      <pre class="language-r">        jitter = jitter,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">176</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       assays = experiment$assays</pre>
+                      <pre class="language-r">        violin = violin</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">177</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     genes &lt;- geneSpecServer(</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">179</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "genes",</pre>
+                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       funs = list(Mean = colMeans),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">181</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_choices = experiment$genes</pre>
+                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">182</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">      id = "plot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">183</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     adtte &lt;- adtteSpecServer(</pre>
+                      <pre class="language-r">      plot_r = plot_r</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "adtte",</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       data = data,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">186</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       adtte_name = "ADTTE",</pre>
+                      <pre class="language-r">    ### REPORTER</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">187</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE",</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">188</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       adtte_vars = list(</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">189</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         aval = "AVAL",</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">190</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         avalu = "AVALU",</pre>
+                      <pre class="language-r">          title = "Boxplot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">191</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         is_event = "is_event",</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">192</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         paramcd = "PARAMCD",</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">193</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         usubjid = "USUBJID"</pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       ),</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">195</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experiment_data = experiment$data,</pre>
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">196</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experiment_name = experiment$name,</pre>
+                      <pre class="language-r">        encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">197</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       assay = assay,</pre>
+                      <pre class="language-r">          "Experiment:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">198</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       genes = genes,</pre>
+                      <pre class="language-r">          input$`experiment-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">199</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       probs = reactive({</pre>
+                      <pre class="language-r">          "\nAssay:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">200</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         0.5</pre>
+                      <pre class="language-r">          input$`assay-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">201</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       })</pre>
+                      <pre class="language-r">          "\nFacetting Variable:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">202</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">          input$`facet-sample_var`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">203</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output$summary &lt;- renderPrint({</pre>
+                      <pre class="language-r">          "\nGenes Selected:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">204</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       binned_adtte_subset &lt;- adtte$binned_adtte_subset()</pre>
+                      <pre class="language-r">          paste0(genes()$get_gene_labels(), collapse = ", "),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">205</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       summary(binned_adtte_subset)</pre>
+                      <pre class="language-r">          "\nGene Summary:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">206</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">          input$`genes-fun_name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">207</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   })</pre>
+                      <pre class="language-r">          "\nJitter:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">208</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">          input$jitter,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">209</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "\nViolin:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">210</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' my_app &lt;- function() {</pre>
+                      <pre class="language-r">          input$violin,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">211</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">          "\nOptional Stratifying Variable:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">212</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">          input$`strat-sample_var`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">213</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     dplyr::mutate(is_event = .data$CNSR == 0)</pre>
+                      <pre class="language-r">          "\nOptional Color Variable:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">214</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          input$`color-sample_var`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">215</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data &lt;- teal_data(</pre>
+                      <pre class="language-r">          "\nOptional Facet Variable:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">216</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     dataset(</pre>
+                      <pre class="language-r">          input$`facet-sample_var`</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">217</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "ADTTE",</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">218</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       adtte,</pre>
+                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">219</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       code = "adtte &lt;- teal.modules.hermes::rADTTE</pre>
+                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">220</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         dplyr::mutate(is_event = .data$CNSR == 0)"</pre>
+                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">221</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     ),</pre>
+                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">222</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     dataset("MAE", mae)</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">223</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">224</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">225</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   app &lt;- init(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">226</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     data = data,</pre>
+                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">227</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     modules = modules(</pre>
+                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">228</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       module(</pre>
+                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">229</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label = "adtteSpec example",</pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">230</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server = server,</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">231</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui = ui,</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">232</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         datanames = "all"</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">233</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">        card</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">234</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">235</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">236</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">237</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">238</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   my_app()</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">241</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' @describeIn tm_g_boxplot sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">adtteSpecServer &lt;- function(id, # nolint</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            data,</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">244</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            mae_name,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">245</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            adtte_name,</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">246</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            adtte_vars,</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">247</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            experiment_data,</pre>
+                      <pre class="language-r">#'   sample_tm_g_boxplot()</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            experiment_name,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">249</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            assay,</pre>
+                      <pre class="language-r">sample_tm_g_boxplot &lt;- function() {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">250</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            genes,</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">251</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            probs) {</pre>
+                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">252</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(id)</pre>
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">253</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">254</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(adtte_name)</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">255</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_adtte_vars(adtte_vars)</pre>
+                      <pre class="language-r">    modules = teal::modules(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">256</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(experiment_data)</pre>
+                      <pre class="language-r">      tm_g_boxplot(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">257</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(experiment_name)</pre>
+                      <pre class="language-r">        label = "boxplot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">258</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(assay)</pre>
+                      <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">259</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(genes)</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">260</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(probs)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">262</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Join ADTTE with gene data.</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">264</td>
-                    <td class="coverage">!</td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/quality.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    adtte_joined &lt;- reactive({</pre>
+                      <pre class="language-r">#' Most Expressed Genes Plot</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">265</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- experiment_data()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">266</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">267</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay &lt;- assay()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">268</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">5</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes &lt;- genes()</pre>
+                      <pre class="language-r">#' This function plots the most expressed genes.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">269</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">270</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate_gene_spec(genes, rownames(experiment_data))</pre>
+                      <pre class="language-r">#' @inheritParams function_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">272</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">#' @return Plot to be displayed in the teal app.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">273</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        genes$returns_vector(),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">274</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        experiment_name,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">275</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">276</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">277</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' library(hermes)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">278</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae &lt;- data[[mae_name]]()</pre>
+                      <pre class="language-r">#' object &lt;- HermesData(summarized_experiment)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">279</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte &lt;- data[[adtte_name]]()</pre>
+                      <pre class="language-r">#' result &lt;- top_gene_plot(object, assay_name = "counts")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">280</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">top_gene_plot &lt;- function(object, assay_name) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">281</td>
+                    <td class="num">18</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae[[experiment_name]] &lt;- experiment_data</pre>
+                      <pre class="language-r">  top_gene &lt;- hermes::top_genes(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">282</td>
+                    <td class="num">19</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      h_km_mae_to_adtte(</pre>
+                      <pre class="language-r">    object = object,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">283</td>
+                    <td class="num">20</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        adtte,</pre>
+                      <pre class="language-r">    assay_name = assay_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">284</td>
+                    <td class="num">21</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae,</pre>
+                      <pre class="language-r">    summary_fun = rowMeans</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">285</td>
+                    <td class="num">23</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        genes = genes,</pre>
+                      <pre class="language-r">  hermes::autoplot(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">286</td>
+                    <td class="num">24</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        experiment_name = experiment_name,</pre>
+                      <pre class="language-r">    top_gene,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">287</td>
+                    <td class="num">25</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay_name = assay,</pre>
+                      <pre class="language-r">    x_lab = "Gene",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">288</td>
+                    <td class="num">26</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        usubjid_var = adtte_vars$usubjid</pre>
+                      <pre class="language-r">    y_lab = paste("Mean", assay_name, "across samples")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">289</td>
+                    <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">290</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">291</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">292</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    gene_col &lt;- reactive({</pre>
+                      <pre class="language-r">#' Correlation Heatmap Plot</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">293</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">31</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      attr(adtte_joined(), "gene_cols")</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">294</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">295</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">296</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # After joining, we recompute available endpoints.</pre>
+                      <pre class="language-r">#' This function plots the correlation heatmap.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">297</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">35</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paramcd_choices &lt;- reactive({</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">298</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">36</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_joined &lt;- adtte_joined()</pre>
+                      <pre class="language-r">#' @inheritParams function_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">299</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">37</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sort(unique(adtte_joined[[adtte_vars$paramcd]])) # Order should not matter.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">300</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @return Plot to be displayed in the teal app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">301</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">302</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Start by disabling selection, will be overriden if there are valid choices.</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">303</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    session$sendCustomMessage(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">304</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">41</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "toggle_dropdown",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">305</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">42</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      list(input_id = session$ns("paramcd"), disabled = TRUE)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">306</td>
+                    <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' library(hermes)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">307</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' object &lt;- HermesData(summarized_experiment)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">308</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Once available endpoints change, we update choices (and also the selection</pre>
+                      <pre class="language-r">#' result &lt;- heatmap_plot(object, assay_name = "counts")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">309</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # if nothing was selected earlier) and warn the user if previous endpoint is</pre>
+                      <pre class="language-r">heatmap_plot &lt;- function(object, assay_name) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">310</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">47</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # not available.</pre>
+                      <pre class="language-r">  heatmap &lt;- hermes::correlate(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">311</td>
+                    <td class="num">48</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(paramcd_choices(), {</pre>
+                      <pre class="language-r">    object = object,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">312</td>
+                    <td class="num">49</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      paramcd_choices &lt;- paramcd_choices()</pre>
+                      <pre class="language-r">    assay_name = assay_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">313</td>
+                    <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">314</td>
+                    <td class="num">51</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      new_selected &lt;- if (is_blank(input$paramcd) || (input$paramcd %in% paramcd_choices)) {</pre>
+                      <pre class="language-r">  hermes::autoplot(heatmap)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">315</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">52</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        input$paramcd</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">316</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">317</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">54</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(type = "warning", paste(</pre>
+                      <pre class="language-r">#' Teal Module for RNA-seq Quality Control</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">318</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">55</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Endpoint", input$paramcd, "not available in this data subset, please",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">319</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">56</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "change filter options or select another endpoint"</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">320</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ))</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">321</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ""</pre>
+                      <pre class="language-r">#' This module adds quality flags, filters by genes and/or samples,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">322</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' normalizes `AnyHermesData` objects and provides interactive plots</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">323</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">60</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      updateSelectizeInput(</pre>
+                      <pre class="language-r">#' for RNA-seq gene expression quality control.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">324</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">61</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "paramcd",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">325</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">62</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = paramcd_choices,</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">326</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">63</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        selected = new_selected,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">327</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        session = session</pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">328</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">329</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      session$sendCustomMessage(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">330</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">67</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "toggle_dropdown",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">331</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">68</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        list(input_id = session$ns("paramcd"), disabled = (length(paramcd_choices) == 0))</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">332</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">333</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">334</td>
+                    <td class="num">71</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">335</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Subset zooming in on a specified endpoint.</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">336</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">73</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    adtte_subset &lt;- reactive({</pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">337</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      endpoint &lt;- input$paramcd</pre>
+                      <pre class="language-r">#'   modules = modules(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">338</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">75</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_joined &lt;- adtte_joined()</pre>
+                      <pre class="language-r">#'     tm_g_quality(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">339</td>
+                    <td class="num">76</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'       label = "Quality Control",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">340</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">77</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">341</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">78</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        endpoint,</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">342</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">79</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "please select an endpoint"</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">343</td>
+                    <td class="num">80</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">344</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Validate that adtte_data is not empty.</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">345</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">346</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        nrow(adtte_joined) &gt; 0,</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">347</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">82</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Joined ADTTE is empty - please relax the filter criteria"</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">348</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">349</td>
+                    <td class="num">84</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">tm_g_quality &lt;- function(label,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">350</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">85</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subset_rows &lt;- adtte_joined[[adtte_vars$paramcd]] == endpoint</pre>
+                      <pre class="language-r">                         mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">351</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">86</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result &lt;- adtte_joined[subset_rows, , drop = FALSE]</pre>
+                      <pre class="language-r">                         exclude_assays = character(),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">352</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">87</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      droplevels(result)</pre>
+                      <pre class="language-r">                         pre_output = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">353</td>
+                    <td class="num">88</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">                         post_output = NULL) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">354</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">89</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">355</td>
+                    <td class="num">90</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    binned_adtte_subset &lt;- reactive({</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">356</td>
+                    <td class="num">91</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_col &lt;- gene_col()</pre>
+                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">357</td>
+                    <td class="num">92</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      probs &lt;- probs()</pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">358</td>
+                    <td class="num">93</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_subset &lt;- adtte_subset()</pre>
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">359</td>
+                    <td class="num">94</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">360</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      result &lt;- tryCatch(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">361</td>
+                    <td class="num">95</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        expr = {</pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">362</td>
+                    <td class="num">96</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          dplyr::mutate(</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">363</td>
+                    <td class="num">97</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            adtte_subset,</pre>
+                      <pre class="language-r">    server = srv_g_quality,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">364</td>
+                    <td class="num">98</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            gene_factor = tern::cut_quantile_bins(</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">365</td>
+                    <td class="num">99</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              adtte_subset[, gene_col],</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">366</td>
+                    <td class="num">100</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              probs = probs</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">367</td>
+                    <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            )</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">368</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">102</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">    ui = ui_g_quality,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">369</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">103</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        },</pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">370</td>
+                    <td class="num">104</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        error = function(e) {</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">371</td>
+                    <td class="num">105</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          if (grepl("Contains duplicated values", e)) {</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">372</td>
+                    <td class="num">106</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            validate(paste(</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">373</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">107</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              "please adjust filters or select (slightly) different quantiles",</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">374</td>
+                    <td class="num">108</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              "to avoid duplicate quantiles"</pre>
+                      <pre class="language-r">    datanames = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">375</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            ))</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">376</td>
+                    <td class="num">110</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          } else {</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">377</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">111</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            stop(e)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">378</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          }</pre>
+                      <pre class="language-r">#' @describeIn tm_g_quality sets up the user interface.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">379</td>
+                    <td class="num">113</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">380</td>
+                    <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">381</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">115</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result</pre>
+                      <pre class="language-r">ui_g_quality &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">382</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">                         data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">383</td>
+                    <td class="num">117</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                         mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">384</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">118</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    time_unit &lt;- reactive({</pre>
+                      <pre class="language-r">                         pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">385</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">119</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_subset &lt;- adtte_subset()</pre>
+                      <pre class="language-r">                         post_output) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">386</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">120</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result &lt;- unique(as.character(adtte_subset[[adtte_vars$avalu]]))</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">121</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assert_string(result)</pre>
+                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">388</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">122</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result</pre>
+                      <pre class="language-r">    encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">389</td>
+                    <td class="num">123</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">      ### Reporter</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">124</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">390</td>
+                    <td class="num">125</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      ###</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">391</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">126</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    list(</pre>
+                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">392</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">127</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      binned_adtte_subset = binned_adtte_subset,</pre>
+                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">393</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">128</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_col = gene_col,</pre>
+                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">394</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_factor = "gene_factor",</pre>
+                      <pre class="language-r">      selectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">395</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">130</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      time_unit = time_unit</pre>
+                      <pre class="language-r">        ns("plot_type"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">396</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">131</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        "Plot Type",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">397</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">132</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">        choices = c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">398</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">133</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          "Histogram",</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/pca.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">134</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for PCA Analysis</pre>
+                      <pre class="language-r">          "Q-Q Plot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">135</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "Density",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">136</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">          "Boxplot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">4</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">137</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "Top Genes Plot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">138</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This module provides an interactive principal components plot and an</pre>
+                      <pre class="language-r">          "Correlation Heatmap"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' interactive heatmap with correlation of principal components with sample</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' variables.</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">141</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">142</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">        condition = "input.plot_type == 'Top Genes Plot' || input.plot_type == 'Correlation Heatmap'",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">143</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">144</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">        assaySpecInput(ns("assay"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">12</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">146</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      tags$label("Gene Filter Settings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">147</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      shinyWidgets::switchInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">148</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">        ns("filter_gene"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">149</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">        value = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">17</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">150</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">        size = "mini"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">18</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">152</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">      conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">20</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">153</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules(</pre>
+                      <pre class="language-r">        condition = "input.filter_gene",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">21</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">154</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     tm_g_pca(</pre>
+                      <pre class="language-r">        ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">155</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       label = "PCA plot",</pre>
+                      <pre class="language-r">        sliderInput(ns("min_cpm"), label = ("Minimum CPM"), min = 1, max = 10, value = 5),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">156</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">        sliderInput(ns("min_cpm_prop"), label = ("Minimum CPM Proportion"), min = 0.01, max = 0.99, value = 0.25),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">157</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">        teal.widgets::optionalSelectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">158</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">          ns("annotate"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">26</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">159</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">          label = "Required Annotations",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">27</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">160</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">          choices = "",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">161</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">          selected = "",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">29</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">162</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">          multiple = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_pca &lt;- function(label,</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">164</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     mae_name,</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">32</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">165</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     exclude_assays = character(),</pre>
+                      <pre class="language-r">      tags$label("Sample Filter Settings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">33</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">166</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     pre_output = NULL,</pre>
+                      <pre class="language-r">      shinyWidgets::switchInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">167</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     post_output = NULL) {</pre>
+                      <pre class="language-r">        ns("filter_sample"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">35</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">168</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  logger::log_info("Initializing tm_g_pca")</pre>
+                      <pre class="language-r">        value = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">36</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">169</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">        size = "mini"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">37</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">170</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">38</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">171</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">      conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">39</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">172</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">        condition = "input.filter_sample",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">173</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">41</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">174</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
+                      <pre class="language-r">        sliderInput(ns("min_corr"), label = ("Minimum Correlation"), min = 0.01, max = 0.99, value = 0.5),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">42</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">175</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
+                      <pre class="language-r">        radioButtons(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">43</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">176</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_pca,</pre>
+                      <pre class="language-r">          ns("min_depth"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">44</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">177</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">          label = "Minimum Depth",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">45</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">178</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">          choices = c("Default", "Specify"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">46</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">179</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">          selected = "Default"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">48</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">181</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_pca,</pre>
+                      <pre class="language-r">        conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">49</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">182</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">          condition = "input.min_depth == 'Specify'",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">50</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">183</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">          ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">51</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">184</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">          sliderInput(ns("min_depth_continuous"), label = NULL, min = 1, max = 10, value = 1)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">52</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">185</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">186</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">187</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">54</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">188</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = mae_name</pre>
+                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">189</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    pre_output = pre_output,</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">190</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    post_output = post_output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">191</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">192</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">193</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_pca sets up the user interface.</pre>
+                      <pre class="language-r">#' @describeIn tm_g_quality sets up the server with reactive graphs.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">195</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">196</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ui_g_pca &lt;- function(id,</pre>
+                      <pre class="language-r">srv_g_quality &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     data,</pre>
+                      <pre class="language-r">                          data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">199</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     mae_name,</pre>
+                      <pre class="language-r">                          filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">200</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     pre_output,</pre>
+                      <pre class="language-r">                          reporter,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">201</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     post_output) {</pre>
+                      <pre class="language-r">                          mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">66</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">202</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">                          exclude_assays) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">67</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">203</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- data[[mae_name]]()</pre>
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">68</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">204</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  experiment_name_choices &lt;- names(mae)</pre>
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">205</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">70</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">207</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tagList(</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">71</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">208</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">72</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">209</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      include_css_files(pattern = "*"),</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">73</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">210</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      encoding = div(</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">74</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">211</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ### Reporter</pre>
+                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">75</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">212</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">      mae_name = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">213</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ###</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">77</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">214</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">79</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">215</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">80</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">216</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">81</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">217</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        conditionalPanel(</pre>
+                      <pre class="language-r">      assays = reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">82</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">218</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          condition = "input.tab_selected == 'PCA'",</pre>
+                      <pre class="language-r">        union(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">83</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">219</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns = ns,</pre>
+                      <pre class="language-r">          experiment$assays(),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">84</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">220</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("color"), "Optional color variable"),</pre>
+                      <pre class="language-r">          # Add all the additional normalized assays.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">221</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selectizeInput(ns("x_var"), "Select X-axis PC", choices = ""),</pre>
+                      <pre class="language-r">          c("cpm", "rpkm", "tpm", "voom", "vst")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">222</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selectizeInput(ns("y_var"), "Select Y-axis PC", choices = "")</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">87</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">      }),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">88</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">224</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::panel_group(</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">225</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          teal.widgets::panel_item(</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">226</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input_id = "settings_item",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">91</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">227</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            collapsed = TRUE,</pre>
+                      <pre class="language-r">    experiment_properties &lt;- eventReactive(experiment$name(), {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">92</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">228</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            title = "Additional Settings",</pre>
+                      <pre class="language-r">      data &lt;- experiment$data()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">93</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">229</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            tags$label("Use only Top Variance Genes"),</pre>
+                      <pre class="language-r">      cpm &lt;- edgeR::cpm(hermes::counts(data))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">230</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            shinyWidgets::switchInput(ns("filter_top"), value = FALSE, size = "mini"),</pre>
+                      <pre class="language-r">      depth &lt;- colSums(hermes::counts(data))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">231</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            conditionalPanel(</pre>
+                      <pre class="language-r">      list(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">96</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">232</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              condition = "input.filter_top",</pre>
+                      <pre class="language-r">        annotations = names(hermes::annotation(data)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">97</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">233</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              ns = ns,</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">98</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">              sliderInput(ns("n_top"), label = "Number of Top Genes", min = 10, max = 5000, value = 500)</pre>
+                      <pre class="language-r">        min_cpm_calc = floor(min(cpm)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">99</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">234</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            ),</pre>
+                      <pre class="language-r">        max_cpm_calc = floor(max(cpm)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">100</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">235</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            conditionalPanel(</pre>
+                      <pre class="language-r">        min_depth_calc = min(depth),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">101</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">236</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              condition = "input.tab_selected == 'PCA'",</pre>
+                      <pre class="language-r">        max_depth_calc = max(depth)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">102</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">237</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              ns = ns,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">103</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">238</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              tags$label("Show Variance %"),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">104</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">239</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              shinyWidgets::switchInput(ns("var_pct"), value = TRUE, size = "mini"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">240</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              tags$label("Show Label"),</pre>
+                      <pre class="language-r">    observeEvent(experiment_properties(), {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">241</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              shinyWidgets::switchInput(ns("label"), value = TRUE, size = "mini")</pre>
+                      <pre class="language-r">      properties &lt;- experiment_properties()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">108</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">243</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            conditionalPanel(</pre>
+                      <pre class="language-r">      teal.widgets::updateOptionalSelectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">109</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">244</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              condition = "input.tab_selected == 'PC and Sample Correlation'",</pre>
+                      <pre class="language-r">        session,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">110</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">245</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              ns = ns,</pre>
+                      <pre class="language-r">        "annotate",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">111</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">246</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              tags$label("Cluster columns"),</pre>
+                      <pre class="language-r">        choices = properties$annotations,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">112</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">247</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              shinyWidgets::switchInput(ns("cluster_columns"), value = FALSE, size = "mini")</pre>
+                      <pre class="language-r">        selected = "WidthBP"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">113</td>
+                    <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            ),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">114</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">            tags$label("View Matrix"),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">115</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">            shinyWidgets::switchInput(ns("show_matrix"), value = TRUE, size = "mini")</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">116</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">249</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">      updateSliderInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">117</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">250</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">        session,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">118</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">251</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">        "min_cpm",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">119</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">252</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      output = div(</pre>
+                      <pre class="language-r">        min = properties$min_cpm_calc,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">120</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">253</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        style = "display:flow-root",</pre>
+                      <pre class="language-r">        max = properties$max_cpm_calc,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">121</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">254</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tabsetPanel(</pre>
+                      <pre class="language-r">        value = properties$min_cpm_calc</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">122</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">255</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          id = ns("tab_selected"),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">123</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">256</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          type = "tabs",</pre>
+                      <pre class="language-r">      updateSliderInput(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">124</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">257</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          tabPanel(</pre>
+                      <pre class="language-r">        session,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">125</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">258</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "PCA",</pre>
+                      <pre class="language-r">        "min_depth_continuous",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">126</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">259</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            column(</pre>
+                      <pre class="language-r">        min = properties$min_depth_calc,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">127</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">260</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              width = 12,</pre>
+                      <pre class="language-r">        max = properties$max_depth_calc,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">128</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">261</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              div(</pre>
+                      <pre class="language-r">        value = properties$min_depth_calc</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">262</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                class = "my-5",</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">130</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">263</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                teal.widgets::plot_with_settings_ui(ns("plot_pca"))</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">131</td>
+                    <td class="num">264</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">132</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">265</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              DT::DTOutput(ns("table_pca"))</pre>
+                      <pre class="language-r">    min_depth_final &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">133</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">266</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            )</pre>
+                      <pre class="language-r">      min_depth &lt;- input$min_depth</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">134</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">267</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ),</pre>
+                      <pre class="language-r">      min_depth_continuous &lt;- input$min_depth_continuous</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">135</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">268</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          tabPanel(</pre>
+                      <pre class="language-r">      if (min_depth == "Specify") {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">136</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">269</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "PC and Sample Correlation",</pre>
+                      <pre class="language-r">        req(min_depth_continuous)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">137</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">270</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            column(</pre>
+                      <pre class="language-r">        min_depth_continuous</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">138</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">271</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              width = 12,</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">139</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">272</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              div(</pre>
+                      <pre class="language-r">        NULL</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">140</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">273</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                class = "my-5",</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">141</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">274</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                teal.widgets::plot_with_settings_ui(ns("plot_cor"))</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">275</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">143</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">276</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    control &lt;- reactive({</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">277</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              DT::DTOutput(ns("table_cor"))</pre>
+                      <pre class="language-r">      min_cpm &lt;- input$min_cpm</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">144</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">278</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            )</pre>
+                      <pre class="language-r">      min_cpm_prop &lt;- input$min_cpm_prop</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">145</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">279</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">      min_corr &lt;- input$min_corr</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">146</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">280</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      min_depth_final &lt;- min_depth_final()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">147</td>
+                    <td class="num">281</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">148</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">282</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">      req(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">149</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">283</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">        min_cpm,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">150</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">284</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        min_cpm_prop,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">151</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">285</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        min_corr</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">152</td>
+                    <td class="num">286</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">153</td>
+                    <td class="num">287</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">154</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_pca sets up the server with reactive graph.</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">155</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">288</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      hermes::control_quality(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">156</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">289</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">        min_cpm = min_cpm,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">157</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">290</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_pca &lt;- function(id,</pre>
+                      <pre class="language-r">        min_cpm_prop = min_cpm_prop,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">158</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">291</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      data,</pre>
+                      <pre class="language-r">        min_corr = min_corr,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">159</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">292</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      filter_panel_api,</pre>
+                      <pre class="language-r">        min_depth = min_depth_final</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">160</td>
+                    <td class="num">293</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      reporter,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">161</td>
+                    <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      mae_name,</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">295</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      exclude_assays) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">163</td>
+                    <td class="num">296</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">    object_flagged &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">164</td>
+                    <td class="num">297</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">      control &lt;- control()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">165</td>
+                    <td class="num">298</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">      object &lt;- experiment$data()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">166</td>
+                    <td class="num">299</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">167</td>
+                    <td class="num">300</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">      already_added &lt;- ("control_quality_flags" %in% names(hermes::metadata(object)))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">168</td>
+                    <td class="num">301</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">      validate(need(!already_added, "Quality flags have already been added to this experiment"))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">169</td>
+                    <td class="num">302</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">      if (any(c("cpm", "rpkm", "tpm", "voom", "vst") %in% SummarizedExperiment::assayNames(object))) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">170</td>
+                    <td class="num">303</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">        showNotification("Original normalized assays will be overwritten", type = "warning")</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">304</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">305</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">171</td>
+                    <td class="num">306</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">      hermes::add_quality_flags(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">172</td>
+                    <td class="num">307</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name</pre>
+                      <pre class="language-r">        object,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">308</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        control = control</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">173</td>
+                    <td class="num">309</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">310</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    })</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">311</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">174</td>
+                    <td class="num">312</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">    object_final &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">175</td>
+                    <td class="num">313</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r">      object_flagged &lt;- object_flagged()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">176</td>
+                    <td class="num">314</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = experiment$assays,</pre>
+                      <pre class="language-r">      filter &lt;- input$filter</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">177</td>
+                    <td class="num">315</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">      annotate &lt;- input$annotate</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">178</td>
+                    <td class="num">316</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">179</td>
+                    <td class="num">317</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    color &lt;- sampleVarSpecServer(</pre>
+                      <pre class="language-r">      req(!is_blank(annotate))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">318</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">180</td>
+                    <td class="num">319</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "color",</pre>
+                      <pre class="language-r">      result &lt;- hermes::filter(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">181</td>
+                    <td class="num">320</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r">        object_flagged,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">182</td>
+                    <td class="num">321</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = experiment$data</pre>
+                      <pre class="language-r">        what = filter,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">183</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">322</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        annotation_required = annotate</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">184</td>
+                    <td class="num">323</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">185</td>
+                    <td class="num">324</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Total number of genes at the moment.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">186</td>
+                    <td class="num">325</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    n_genes &lt;- reactive({</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">187</td>
+                    <td class="num">326</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
+                      <pre class="language-r">        nrow(result) &gt;= 2,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">188</td>
+                    <td class="num">327</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      nrow(experiment_data)</pre>
+                      <pre class="language-r">        "Please change gene filters to ensure that there are at least 2 genes"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">189</td>
+                    <td class="num">328</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">190</td>
+                    <td class="num">329</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
+                  <tr class="missed">
+                    <td class="num">330</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      hermes::normalize(result)</pre>
+                    </td>
+                  </tr>
                   <tr class="never">
-                    <td class="num">191</td>
+                    <td class="num">331</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the total number changes or gene filter is activated, update slider max.</pre>
+                      <pre class="language-r">    })</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">332</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">192</td>
+                    <td class="num">333</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(list(n_genes(), input$filter_top), {</pre>
+                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">193</td>
+                    <td class="num">334</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      n_genes &lt;- n_genes()</pre>
+                      <pre class="language-r">      object_final &lt;- object_final()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">194</td>
+                    <td class="num">335</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_top &lt;- input$filter_top</pre>
+                      <pre class="language-r">      plot_type &lt;- input$plot_type</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">195</td>
+                    <td class="num">336</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (filter_top) {</pre>
+                      <pre class="language-r">      assay_name &lt;- assay()</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">337</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">196</td>
+                    <td class="num">338</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        n_top &lt;- input$n_top</pre>
+                      <pre class="language-r">      switch(plot_type,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">197</td>
+                    <td class="num">339</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        updateSliderInput(</pre>
+                      <pre class="language-r">        "Histogram" = hermes::draw_libsize_hist(object_final),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">198</td>
+                    <td class="num">340</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session = session,</pre>
+                      <pre class="language-r">        "Density" = hermes::draw_libsize_densities(object_final),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">199</td>
+                    <td class="num">341</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          inputId = "n_top",</pre>
+                      <pre class="language-r">        "Q-Q Plot" = hermes::draw_libsize_qq(object_final),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">200</td>
+                    <td class="num">342</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          value = min(n_top, n_genes),</pre>
+                      <pre class="language-r">        "Boxplot" = hermes::draw_nonzero_boxplot(object_final),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">201</td>
+                    <td class="num">343</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          max = n_genes</pre>
+                      <pre class="language-r">        "Top Genes Plot" = top_gene_plot(object_final, assay_name = assay_name),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">202</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">344</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">        "Correlation Heatmap" = heatmap_plot(object_final, assay_name = assay_name)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">203</td>
+                    <td class="num">345</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">204</td>
+                    <td class="num">346</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">205</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">347</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">206</td>
+                    <td class="num">348</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the chosen experiment or assay name changes, recompute the PC.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">207</td>
+                    <td class="num">349</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pca_result &lt;- reactive({</pre>
+                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">208</td>
+                    <td class="num">350</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
+                      <pre class="language-r">      id = "plot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">209</td>
+                    <td class="num">351</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_top &lt;- input$filter_top</pre>
+                      <pre class="language-r">      plot_r = plot_r</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">210</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">352</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      n_top &lt;- input$n_top</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">211</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">353</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay_name &lt;- assay()</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">212</td>
+                    <td class="num">354</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    ### REPORTER</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">213</td>
+                    <td class="num">355</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(hermes::is_hermes_data(experiment_data), "please use HermesData() on input experiments"))</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">214</td>
+                    <td class="num">356</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(isTRUE(assay_name %in% SummarizedExperiment::assayNames(experiment_data)))</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">215</td>
+                    <td class="num">357</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">216</td>
+                    <td class="num">358</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ncol(experiment_data) &gt; 2,</pre>
+                      <pre class="language-r">          title = "Quality Control Plot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">217</td>
+                    <td class="num">359</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Sample size is too small. PCA needs more than 2 samples."</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">218</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">219</td>
+                    <td class="num">360</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">          description = tools::toTitleCase(input$plot_type),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">220</td>
+                    <td class="num">361</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        nrow(experiment_data) &gt; 1,</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">221</td>
+                    <td class="num">362</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Number of genes is too small. PCA needs more than 1 gene."</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">222</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">363</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">224</td>
+                    <td class="num">364</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::calc_pca(experiment_data, assay_name, n_top = if (filter_top) n_top else NULL)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">225</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">226</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">227</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    # When experiment or assay name changes, update choices for PCs in x_var and y_var.</pre>
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">228</td>
+                    <td class="num">365</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(pca_result(), {</pre>
+                      <pre class="language-r">        encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">229</td>
+                    <td class="num">366</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pca_result_x &lt;- pca_result()$x</pre>
+                      <pre class="language-r">          "Experiment:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">230</td>
+                    <td class="num">367</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pc_choices &lt;- seq_len(ncol(pca_result_x))</pre>
+                      <pre class="language-r">          input$`experiment-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">231</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">368</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          "\nPlot Type:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">232</td>
+                    <td class="num">369</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id_names &lt;- c("x_var", "y_var")</pre>
+                      <pre class="language-r">          input$plot_type,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">233</td>
+                    <td class="num">370</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      for (i in seq_along(id_names)) {</pre>
+                      <pre class="language-r">          "\nAssay:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">234</td>
+                    <td class="num">371</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        updateSelectizeInput(</pre>
+                      <pre class="language-r">          input$`assay-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">235</td>
+                    <td class="num">372</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session,</pre>
+                      <pre class="language-r">          "\nShow Gene Filter Settings:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">236</td>
+                    <td class="num">373</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          id_names[i],</pre>
+                      <pre class="language-r">          input$filter_gene,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">237</td>
+                    <td class="num">374</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = pc_choices,</pre>
+                      <pre class="language-r">          "\nMinimum CPM:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">238</td>
+                    <td class="num">375</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = pc_choices[i]</pre>
+                      <pre class="language-r">          input$min_cpm,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">239</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">376</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">          "\nMinimum CPM Proportion:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">240</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">377</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">          input$min_cpm_prop,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">241</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">378</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          "\nRequired Annotations:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">242</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">379</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          paste(input$annotate, collapse = ", "),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">243</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">380</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Compute correlation of PC with sample variables.</pre>
+                      <pre class="language-r">          "\nShow Sample Filter Settings:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">244</td>
+                    <td class="num">381</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    cor_result &lt;- reactive({</pre>
+                      <pre class="language-r">          input$filter_sample,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">245</td>
+                    <td class="num">382</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pca_result &lt;- pca_result()</pre>
+                      <pre class="language-r">          "\nMinimum Correlation:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">246</td>
+                    <td class="num">383</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
+                      <pre class="language-r">          input$min_corr,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">247</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">384</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          "\nMinimum Depth:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">248</td>
+                    <td class="num">385</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::correlate(pca_result, experiment_data)</pre>
+                      <pre class="language-r">          input$min_depth,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">249</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">386</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          "\nMinimum Depth Value:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">250</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">387</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          input$min_depth_continuous</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">251</td>
+                    <td class="num">388</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Compute &amp; display PCA matrix table if show_matrix is TRUE.</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">252</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    show_matrix_pca &lt;- reactive({</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">253</td>
+                    <td class="num">389</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (input$show_matrix) {</pre>
+                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">254</td>
+                    <td class="num">390</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        pca_result_x &lt;- pca_result()$x</pre>
+                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">255</td>
+                    <td class="num">391</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        pca_result_x &lt;- round(pca_result_x, 3)</pre>
+                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">256</td>
+                    <td class="num">392</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        as.data.frame(pca_result_x)</pre>
+                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">257</td>
+                    <td class="num">393</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">258</td>
+                    <td class="num">394</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        NULL</pre>
+                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">259</td>
+                    <td class="num">395</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">260</td>
+                    <td class="num">396</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">261</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">397</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">262</td>
+                    <td class="num">398</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$table_pca &lt;- DT::renderDT({</pre>
+                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">263</td>
+                    <td class="num">399</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      show_matrix_pca &lt;- show_matrix_pca()</pre>
+                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">264</td>
+                    <td class="num">400</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      DT::datatable(</pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">265</td>
+                    <td class="num">401</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_matrix_pca,</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">266</td>
+                    <td class="num">402</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        rownames = TRUE,</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">403</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">267</td>
+                    <td class="num">404</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        options = list(scrollX = TRUE, pageLength = 30, lengthMenu = c(5, 15, 30, 100)),</pre>
+                      <pre class="language-r">        card</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">405</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">268</td>
+                    <td class="num">406</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        caption = "PCA Matrix"</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">269</td>
+                    <td class="num">407</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">270</td>
+                    <td class="num">408</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">409</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">272</td>
+                    <td class="num">410</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Compute &amp; display correlation matrix if show_matrix is TRUE</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">273</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">411</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    show_matrix_cor &lt;- reactive({</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">274</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">412</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (input$show_matrix) {</pre>
+                      <pre class="language-r">#' @describeIn tm_g_quality sample module function.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">275</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">413</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cor_result &lt;- cor_result()</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">276</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">414</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cor_result &lt;- round(cor_result, 3)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">277</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">415</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        as.data.frame(cor_result)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">278</td>
+                    <td class="num">416</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">279</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">417</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' if (interactive()) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">418</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        NULL</pre>
+                      <pre class="language-r">#'   sample_tm_g_quality()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">280</td>
+                    <td class="num">419</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">281</td>
+                    <td class="num">420</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">sample_tm_g_quality &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">282</td>
+                    <td class="num">421</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$table_cor &lt;- DT::renderDT({</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">283</td>
+                    <td class="num">422</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      show_matrix_cor &lt;- show_matrix_cor()</pre>
+                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">284</td>
+                    <td class="num">423</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      DT::datatable(</pre>
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">285</td>
+                    <td class="num">424</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        show_matrix_cor,</pre>
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">286</td>
+                    <td class="num">425</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        rownames = TRUE,</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">287</td>
+                    <td class="num">426</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        options = list(scrollX = TRUE, pageLength = 30, lengthMenu = c(5, 15, 30, 100)),</pre>
+                      <pre class="language-r">    modules = teal::modules(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">288</td>
+                    <td class="num">427</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        caption = "PC and Sample Correlation Matrix"</pre>
+                      <pre class="language-r">      tm_g_quality(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">289</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">428</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">        label = "quality",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">290</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">429</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">291</td>
+                    <td class="num">430</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">292</td>
+                    <td class="num">431</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Render plot PCA output.</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">293</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    plot_pca &lt;- reactive({</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">294</td>
+                    <td class="num">432</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Resolve all reactivity.</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">295</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      pca_result &lt;- pca_result()</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">296</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">297</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      x_var &lt;- as.numeric(input$x_var)</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">298</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      y_var &lt;- as.numeric(input$y_var)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">299</td>
+                    <td class="num">433</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data &lt;- as.data.frame(SummarizedExperiment::colData(color$experiment_data()))</pre>
+                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">300</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">434</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      color_var &lt;- color$sample_var()</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">301</td>
-                    <td class="coverage">!</td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/adtteSpec.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay_name &lt;- assay()</pre>
+                      <pre class="language-r">#' Data Preprocessing for `ADTTE` Module</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">302</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      var_pct &lt;- input$var_pct</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">303</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      label &lt;- input$label</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">304</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">305</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Require which states need to be truthy.</pre>
+                      <pre class="language-r">#' A function to help with merging of MAE to `ADTTE`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">306</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">307</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay_name,</pre>
+                      <pre class="language-r">#' @inheritParams function_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">308</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        # Note: The following statements are important to make sure the UI inputs have been updated.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">309</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        isTRUE(assay_name %in% SummarizedExperiment::assayNames(experiment_data)),</pre>
+                      <pre class="language-r">#' @return A data frame containing all columns/rows from `adtte` that match</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">310</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is.null(color_var) || isTRUE(color_var %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                      <pre class="language-r">#'   by subject ID with the row names of the MAE and have the gene samples available</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">311</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cancelOutput = FALSE</pre>
+                      <pre class="language-r">#'   in the given experiment. The attribute `gene_cols` contains the column names</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">312</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'   for the gene columns.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">313</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">314</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Validate and give useful messages to the user. Note: no need to duplicate here req() from above.</pre>
+                      <pre class="language-r">#' @note The final gene column names can start with a different string than</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">315</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(x_var != y_var, "please select two different principal components"))</pre>
+                      <pre class="language-r">#'   the original gene IDs (or labels), in particular white space and colons are removed.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">316</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">317</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">17</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::autoplot(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">318</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">18</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object = pca_result,</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">319</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay_name = assay_name,</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">320</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">20</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        x = x_var,</pre>
+                      <pre class="language-r">#' adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">321</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        y = y_var,</pre>
+                      <pre class="language-r">#'   dplyr::mutate(CNSR = as.logical(CNSR))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">322</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        data = data,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">323</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">23</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        colour = color_var,</pre>
+                      <pre class="language-r">#' new_adtte &lt;- h_km_mae_to_adtte(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">324</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">24</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        variance_percentage = var_pct,</pre>
+                      <pre class="language-r">#'   adtte,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">325</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = label,</pre>
+                      <pre class="language-r">#'   mae,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">326</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">26</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label.repel = label,</pre>
+                      <pre class="language-r">#'   genes = hermes::gene_spec("GeneID:1820"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">327</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label.show.legend = FALSE</pre>
+                      <pre class="language-r">#'   experiment_name = "hd2"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">328</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">329</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' new_adtte2 &lt;- h_km_mae_to_adtte(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">330</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$plot_pca &lt;- renderPlot(plot_pca())</pre>
+                      <pre class="language-r">#'   adtte,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">331</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   mae,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">332</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws_pca &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">#'   genes = hermes::gene_spec(c("GeneID:1820", "GeneID:94115"), fun = colMeans),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">333</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">33</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot_pca",</pre>
+                      <pre class="language-r">#'   experiment_name = "hd2"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">334</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = plot_pca</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">335</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' new_adtte3 &lt;- h_km_mae_to_adtte(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">336</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   adtte,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">337</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # render correlation heatmap</pre>
+                      <pre class="language-r">#'   mae,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">338</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">38</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_cor &lt;- reactive({</pre>
+                      <pre class="language-r">#'   genes = hermes::gene_spec(c(A = "GeneID:1820", B = "GeneID:94115")),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">339</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Resolve all reactivity.</pre>
+                      <pre class="language-r">#'   experiment_name = "hd2"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">340</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">40</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cor_result &lt;- cor_result()</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">341</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">41</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cluster_columns &lt;- input$cluster_columns</pre>
+                      <pre class="language-r">h_km_mae_to_adtte &lt;- function(adtte,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">342</td>
+                    <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                              mae,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">343</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">43</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">                              genes,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">344</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">44</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        !any(is.na(cor_result)),</pre>
+                      <pre class="language-r">                              experiment_name = "hd1",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">345</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">45</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Obtained NA results in the correlation matrix, therefore no plot can be produced"</pre>
+                      <pre class="language-r">                              assay_name = "counts",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">346</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">                              usubjid_var = "USUBJID") {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">347</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">47</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::autoplot(</pre>
+                      <pre class="language-r">  assert_class(mae, "MultiAssayExperiment")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">348</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">48</td>
+                    <td class="coverage">11<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object = cor_result,</pre>
+                      <pre class="language-r">  assert_string(experiment_name)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">349</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">49</td>
+                    <td class="coverage">10<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cluster_columns = cluster_columns</pre>
+                      <pre class="language-r">  assert_string(usubjid_var)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">350</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">50</td>
+                    <td class="coverage">10<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  assert_names(names(adtte), must.include = usubjid_var)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">351</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">352</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  # Check subject ID across experiment, sample map, and MAE colData.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">353</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">53</td>
+                    <td class="coverage">10<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws_cor &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">  mae_samplemap &lt;- MultiAssayExperiment::sampleMap(mae)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">354</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">54</td>
+                    <td class="coverage">10<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot_cor",</pre>
+                      <pre class="language-r">  samplemap_experiment &lt;- mae_samplemap[mae_samplemap$assay == experiment_name, ]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">355</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">55</td>
+                    <td class="coverage">10<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = plot_cor</pre>
+                      <pre class="language-r">  sm_usubjid &lt;- as.character(samplemap_experiment$primary)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">356</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">57</td>
+                    <td class="coverage">10<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  hd &lt;- suppressWarnings(MultiAssayExperiment::getWithColData(mae, experiment_name))</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">58</td>
+                    <td class="coverage">9<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_class(hd, "AnyHermesData")</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">59</td>
+                    <td class="coverage">9<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  hd_usubjid &lt;- as.character(SummarizedExperiment::colData(hd)[[usubjid_var]])</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">357</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">358</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">61</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
+                      <pre class="language-r">  assert_subset(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">359</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">62</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">    x = hd_usubjid,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">360</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">63</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">    choices = sm_usubjid</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">361</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">362</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">65</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("PCA")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">363</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">66</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("PCA", "header2")</pre>
+                      <pre class="language-r">  mae_coldata &lt;- MultiAssayExperiment::colData(mae)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">364</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">67</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">  if (usubjid_var %in% colnames(mae_coldata)) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">365</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r">    mae_usubjid &lt;- as.character(mae_coldata[[usubjid_var]])</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">366</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">69</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (input$tab_selected == "PCA") {</pre>
+                      <pre class="language-r">    assert_subset(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">367</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">70</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          encodings_list &lt;- list(</pre>
+                      <pre class="language-r">      x = sm_usubjid,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">368</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">8<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "Experiment:",</pre>
+                      <pre class="language-r">      choices = mae_usubjid</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">369</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">72</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$`experiment-name`,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">370</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">73</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nAssay:",</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">371</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$`assay-name`,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">372</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nOptional Color Variable:",</pre>
+                      <pre class="language-r">  gene_data &lt;- hermes::col_data_with_genes(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">373</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$`color-sample_var`,</pre>
+                      <pre class="language-r">    object = hd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">374</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nX-axis PC:",</pre>
+                      <pre class="language-r">    assay_name = assay_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">375</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$x_var,</pre>
+                      <pre class="language-r">    genes = genes</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">376</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">79</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nY-axis PC:",</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">377</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$y_var,</pre>
+                      <pre class="language-r">  merged_adtte &lt;- hermes::inner_join_cdisc(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">378</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">81</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nUse Top Variance Genes:",</pre>
+                      <pre class="language-r">    gene_data = gene_data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">379</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">82</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$filter_top,</pre>
+                      <pre class="language-r">    cdisc_data = adtte,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">380</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">83</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nNumber of Top Genes:",</pre>
+                      <pre class="language-r">    patient_key = usubjid_var</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">381</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">84</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$n_top,</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">382</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nShow Variance %:",</pre>
+                      <pre class="language-r">  structure(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">383</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$var_pct,</pre>
+                      <pre class="language-r">    merged_adtte,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">384</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">87</td>
+                    <td class="coverage">5<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nShow Matrix:",</pre>
+                      <pre class="language-r">    gene_cols = attr(gene_data, "gene_cols")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">385</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">88</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$show_matrix,</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">386</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">89</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nShow Label:",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">90</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$label</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">388</td>
+                    <td class="num">91</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">#' Module Input for `ADTTE` Specification</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">389</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">92</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">93</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">390</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">94</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">391</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">95</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">#' This defines the input for the `ADTTE` specification.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">392</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">96</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          } else {</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">394</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">98</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">#' @param label_paramcd (`string`)\cr label for the endpoint (`PARAMCD`) selection.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">395</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">396</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">100</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">#' @return The UI part.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">397</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">101</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">#' @seealso [adtteSpecServer()] for the module server and a complete example.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">398</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">102</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_plot(plot_pca(), dim = pws_pca$dim())</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">399</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">103</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Table", "header3")</pre>
+                      <pre class="language-r">adtteSpecInput &lt;- function(inputId, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">400</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">104</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_table(show_matrix_pca())</pre>
+                      <pre class="language-r">                           label_paramcd = "Select Endpoint") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">401</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">105</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">  assert_string(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">402</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          encodings_list &lt;- list(</pre>
+                      <pre class="language-r">  assert_string(label_paramcd, min.chars = 1L)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">403</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">107</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "Experiment:",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">404</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">108</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$`experiment-name`,</pre>
+                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">405</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">109</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nAssay:",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">406</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">110</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$`assay-name`,</pre>
+                      <pre class="language-r">  tagList(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">407</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">111</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nUse Top Variance Genes:",</pre>
+                      <pre class="language-r">    selectizeInput(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">408</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">112</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$filter_top,</pre>
+                      <pre class="language-r">      inputId = ns("paramcd"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">409</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">113</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nNumber of Top Genes:",</pre>
+                      <pre class="language-r">      label = label_paramcd,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">410</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$top_n,</pre>
+                      <pre class="language-r">      choices = "",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">411</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">115</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nCluster Columns:",</pre>
+                      <pre class="language-r">      options = list(placeholder = "- Nothing selected -")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">412</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">116</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            paste0(input$cluster_columns, collapse = ", "),</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">413</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">117</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "\nShow Matrix:",</pre>
+                      <pre class="language-r">    include_js_files("dropdown.js")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">414</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">118</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            input$show_matrix</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">415</td>
+                    <td class="num">119</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">416</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">120</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">417</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">121</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">#' Module Server for `ADTTE` Specification</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">418</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">122</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">419</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">123</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">420</td>
+                    <td class="num">124</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          } else {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">421</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">125</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">#' This defines the server part for the `ADTTE` specification. The resulting data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">422</td>
+                    <td class="num">126</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          }</pre>
+                      <pre class="language-r">#' set `binned_adtte_subset` contains the subset of `ADTTE` selected by the time-to-event</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">423</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' endpoint, joined together with the gene information extracted from specified assay</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">424</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">128</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">#' and experiment, as numeric and factor columns. The factor column is created by binning</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">425</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">129</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">#' the numeric column according to the quantile cutoffs specified in `probs`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">426</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">130</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_plot(plot_cor())</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">427</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">131</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_plot(plot_cor(), dim = pws_cor$dim())</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">428</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">132</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Table", "header3")</pre>
+                      <pre class="language-r">#' @param experiment_data (reactive `AnyHermesData`)\cr input experiment.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">429</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">133</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_table(show_matrix_cor())</pre>
+                      <pre class="language-r">#' @param experiment_name (reactive `string`)\cr name of the input experiment.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">430</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#' @param assay (reactive `string`)\cr name of the assay.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">431</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">135</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">#' @param genes (reactive `GeneSpec`)\cr gene specification.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">432</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">136</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">#' @param probs (reactive `numeric`)\cr probabilities to bin the gene or gene signature</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">433</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">137</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r">#'   into.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">434</td>
+                    <td class="num">138</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">435</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">139</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
+                      <pre class="language-r">#' @return List with the following elements:</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">436</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'   - `binned_adtte_subset`: reactive containing the joined `ADTTE` and gene data.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">437</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">141</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
+                      <pre class="language-r">#'   - `gene_col`: reactive containing the string with the column name of the original</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">438</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#'        numeric gene variable.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">439</td>
+                    <td class="num">143</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r">#'   - `gene_factor`: string with the variable name for the binned gene data.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">440</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">#'   - `time_unit`: reactive string with the time unit for the current subset.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">441</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">442</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @seealso [adtteSpecInput()] for the module UI.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">443</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_pca sample module function.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">444</td>
+                    <td class="num">148</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">445</td>
+                    <td class="num">149</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">446</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' ui &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">447</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r">#'                data) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">448</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">449</td>
+                    <td class="num">154</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_pca()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">450</td>
+                    <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">451</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_pca &lt;- function() {</pre>
+                      <pre class="language-r">#'     encoding = div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">452</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">157</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">#'       experimentSpecInput(ns("experiment"), data = data, mae_name = "MAE"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">453</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">158</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">#'       assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">454</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">159</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
+                      <pre class="language-r">#'       geneSpecInput(ns("genes"), funs = list(Mean = colMeans)),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">455</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">160</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                      <pre class="language-r">#'       adtteSpecInput(ns("adtte"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">456</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">161</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r">#'     ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">457</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">162</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = teal::modules(</pre>
+                      <pre class="language-r">#'     output = verbatimTextOutput(ns("summary"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">458</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">163</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tm_g_pca(</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">459</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">164</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = "pca",</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">460</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">165</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae_name = "MAE"</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">461</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' server &lt;- function(id, data, filter_panel_api) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">462</td>
+                    <td class="num">167</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">463</td>
+                    <td class="num">168</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#'     experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">464</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">169</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">#'       "experiment",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">465</td>
+                    <td class="num">170</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'       data = data,</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/forestplot.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for Survival Forest Plot</pre>
+                      <pre class="language-r">#'       filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">175</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This module provides an interactive survival forest plot.</pre>
+                      <pre class="language-r">#'       "assay",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">176</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       assays = experiment$assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">177</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     genes &lt;- geneSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">179</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">#'       "genes",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       funs = list(Mean = colMeans),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">181</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'       gene_choices = experiment$genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">12</td>
+                    <td class="num">182</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#'     adtte &lt;- adtteSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">#'       "adtte",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">#'       data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">186</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dplyr::mutate(is_event = (.data$CNSR == 0))</pre>
+                      <pre class="language-r">#'       adtte_name = "ADTTE",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">187</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       mae_name = "MAE",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">18</td>
+                    <td class="num">188</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(</pre>
+                      <pre class="language-r">#'       adtte_vars = list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">189</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dataset(</pre>
+                      <pre class="language-r">#'         aval = "AVAL",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">190</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     "ADTTE",</pre>
+                      <pre class="language-r">#'         avalu = "AVALU",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">191</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     adtte,</pre>
+                      <pre class="language-r">#'         is_event = "is_event",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">192</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">#'         paramcd = "PARAMCD",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">23</td>
+                    <td class="num">193</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       dplyr::mutate(is_event = (.data$CNSR == 0))"</pre>
+                      <pre class="language-r">#'         usubjid = "USUBJID"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">24</td>
+                    <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ),</pre>
+                      <pre class="language-r">#'       ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">25</td>
+                    <td class="num">195</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dataset("MAE", mae)</pre>
+                      <pre class="language-r">#'       experiment_data = experiment$data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">196</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">#'       experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r">#'       assay = assay,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">#'       genes = genes,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">199</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules(</pre>
+                      <pre class="language-r">#'       probs = reactive({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">200</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     tm_g_forest_tte(</pre>
+                      <pre class="language-r">#'         0.5</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">201</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       label = "forestplot",</pre>
+                      <pre class="language-r">#'       })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">202</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       adtte_name = "ADTTE",</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">203</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">#'     output$summary &lt;- renderPrint({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">204</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">#'       binned_adtte_subset &lt;- adtte$binned_adtte_subset()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">#'       summary(binned_adtte_subset)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">207</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">#'   })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">208</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">209</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">40</td>
+                    <td class="num">210</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_forest_tte &lt;- function(label,</pre>
+                      <pre class="language-r">#' my_app &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">211</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            adtte_name,</pre>
+                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">212</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            mae_name,</pre>
+                      <pre class="language-r">#'   adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">213</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            adtte_vars = list(</pre>
+                      <pre class="language-r">#'     dplyr::mutate(is_event = .data$CNSR == 0)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">214</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              aval = "AVAL",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              is_event = "is_event",</pre>
+                      <pre class="language-r">#'   data &lt;- teal_data(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">216</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              paramcd = "PARAMCD",</pre>
+                      <pre class="language-r">#'     dataset(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">217</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              usubjid = "USUBJID",</pre>
+                      <pre class="language-r">#'       "ADTTE",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">218</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              avalu = "AVALU"</pre>
+                      <pre class="language-r">#'       adtte,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">219</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            ),</pre>
+                      <pre class="language-r">#'       code = "adtte &lt;- teal.modules.hermes::rADTTE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">50</td>
+                    <td class="num">220</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            exclude_assays = "counts",</pre>
+                      <pre class="language-r">#'         dplyr::mutate(is_event = .data$CNSR == 0)"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">221</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            summary_funs = list(</pre>
+                      <pre class="language-r">#'     ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">222</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              Mean = colMeans,</pre>
+                      <pre class="language-r">#'     dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              Median = matrixStats::colMedians,</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">224</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              Max = matrixStats::colMaxs</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">225</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            ),</pre>
+                      <pre class="language-r">#'   app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">226</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            pre_output = NULL,</pre>
+                      <pre class="language-r">#'     data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">227</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            post_output = NULL,</pre>
+                      <pre class="language-r">#'     modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">228</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            plot_height = c(600L, 200L, 2000L),</pre>
+                      <pre class="language-r">#'       module(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">229</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            plot_width = c(1360L, 500L, 2000L)) {</pre>
+                      <pre class="language-r">#'         label = "adtteSpec example",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">60</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">230</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  logger::log_info("Initializing tm_g_forest_tte")</pre>
+                      <pre class="language-r">#'         server = server,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">61</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">231</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">#'         ui = ui,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">62</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">232</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(adtte_name)</pre>
+                      <pre class="language-r">#'         datanames = "all"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">63</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">233</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">64</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">234</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_adtte_vars(adtte_vars)</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">65</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">235</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">66</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">236</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_summary_funs(summary_funs)</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">67</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">237</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">68</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">238</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">70</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">240</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
+                      <pre class="language-r">#'   my_app()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">71</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">241</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">72</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">242</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_forest_tte,</pre>
+                      <pre class="language-r">adtteSpecServer &lt;- function(id, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">73</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">243</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">                            data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">74</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">244</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = adtte_name,</pre>
+                      <pre class="language-r">                            mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">75</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">245</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">                            adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">76</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">246</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
+                      <pre class="language-r">                            adtte_vars,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">77</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">247</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays,</pre>
+                      <pre class="language-r">                            experiment_data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">78</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">248</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">                            experiment_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">79</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">249</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_height = plot_height,</pre>
+                      <pre class="language-r">                            assay,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">80</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">250</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_width = plot_width</pre>
+                      <pre class="language-r">                            genes,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">251</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">                            probs) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">82</td>
+                    <td class="num">252</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_forest_tte,</pre>
+                      <pre class="language-r">  assert_string(id)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">83</td>
+                    <td class="num">253</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">84</td>
+                    <td class="num">254</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = adtte_name,</pre>
+                      <pre class="language-r">  assert_string(adtte_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">85</td>
+                    <td class="num">255</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">  assert_adtte_vars(adtte_vars)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">86</td>
+                    <td class="num">256</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">  assert_reactive(experiment_data)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">87</td>
+                    <td class="num">257</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">  assert_reactive(experiment_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">88</td>
+                    <td class="num">258</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">89</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">  assert_reactive(assay)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">90</td>
+                    <td class="num">259</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = c(adtte_name, mae_name)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">91</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  assert_reactive(genes)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">92</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">260</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  assert_reactive(probs)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">93</td>
+                    <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">94</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_forest_tte sets up the user interface.</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">95</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">96</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">97</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">ui_g_forest_tte &lt;- function(id,</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">98</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">262</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            data,</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            adtte_name,</pre>
+                      <pre class="language-r">    # Join ADTTE with gene data.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">100</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">264</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            mae_name,</pre>
+                      <pre class="language-r">    adtte_joined &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">101</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">265</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            summary_funs,</pre>
+                      <pre class="language-r">      experiment_data &lt;- experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">102</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">266</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            pre_output,</pre>
+                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">103</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">267</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            post_output) {</pre>
+                      <pre class="language-r">      assay &lt;- assay()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">104</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">268</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">      genes &lt;- genes()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">269</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">270</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    encoding = div(</pre>
+                      <pre class="language-r">      validate_gene_spec(genes, rownames(experiment_data))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">271</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ### Reporter</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">108</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">272</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">      req(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">109</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">273</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ###</pre>
+                      <pre class="language-r">        genes$returns_vector(),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">110</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">274</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r">        experiment_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">111</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">275</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r">        assay</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">112</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">276</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">113</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">277</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">114</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">278</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      geneSpecInput(ns("genes"), summary_funs),</pre>
+                      <pre class="language-r">      mae &lt;- data[[mae_name]]()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">115</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">279</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of ADTTE:", tags$code(adtte_name)),</pre>
+                      <pre class="language-r">      adtte &lt;- data[[adtte_name]]()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">116</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">280</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtteSpecInput(ns("adtte")),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">117</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">281</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::panel_group(</pre>
+                      <pre class="language-r">      mae[[experiment_name]] &lt;- experiment_data</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">118</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">282</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::panel_item(</pre>
+                      <pre class="language-r">      h_km_mae_to_adtte(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">119</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">283</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input_id = "settings_item",</pre>
+                      <pre class="language-r">        adtte,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">120</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">284</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          collapsed = TRUE,</pre>
+                      <pre class="language-r">        mae,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">121</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">285</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = "Additional Settings",</pre>
+                      <pre class="language-r">        genes = genes,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">122</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">286</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sliderInput(ns("probs"), label = ("Probability Cutoff"), min = 0.01, max = 0.99, value = 0.5),</pre>
+                      <pre class="language-r">        experiment_name = experiment_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">123</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">287</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("subgroups"), "Select Categorical Subgroup Variable")</pre>
+                      <pre class="language-r">        assay_name = assay,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">124</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">288</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">        usubjid_var = adtte_vars$usubjid</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">289</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">290</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">127</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">128</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">291</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pre_output = pre_output,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">292</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    post_output = post_output</pre>
+                      <pre class="language-r">    gene_col &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">130</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">293</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      attr(adtte_joined(), "gene_cols")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">131</td>
+                    <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">132</td>
+                    <td class="num">295</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">296</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_forest_tte sets up the server with reactive graph.</pre>
+                      <pre class="language-r">    # After joining, we recompute available endpoints.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">134</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">297</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">    paramcd_choices &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">135</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">298</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      adtte_joined &lt;- adtte_joined()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">136</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">299</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_forest_tte &lt;- function(id,</pre>
+                      <pre class="language-r">      sort(unique(adtte_joined[[adtte_vars$paramcd]])) # Order should not matter.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">300</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             data,</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">138</td>
+                    <td class="num">301</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             filter_panel_api,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">139</td>
+                    <td class="num">302</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             reporter,</pre>
+                      <pre class="language-r">    # Start by disabling selection, will be overriden if there are valid choices.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">140</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">303</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             adtte_name,</pre>
+                      <pre class="language-r">    session$sendCustomMessage(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">141</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">304</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             mae_name,</pre>
+                      <pre class="language-r">      "toggle_dropdown",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">142</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">305</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             adtte_vars,</pre>
+                      <pre class="language-r">      list(input_id = session$ns("paramcd"), disabled = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">306</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             exclude_assays,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">307</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             summary_funs,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">308</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             plot_height,</pre>
+                      <pre class="language-r">    # Once available endpoints change, we update choices (and also the selection</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">146</td>
+                    <td class="num">309</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             plot_width) {</pre>
+                      <pre class="language-r">    # if nothing was selected earlier) and warn the user if previous endpoint is</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">147</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">310</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">    # not available.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">148</td>
+                    <td class="num">311</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">    observeEvent(paramcd_choices(), {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">149</td>
+                    <td class="num">312</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">      paramcd_choices &lt;- paramcd_choices()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">150</td>
+                    <td class="num">313</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">151</td>
+                    <td class="num">314</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">      new_selected &lt;- if (is_blank(input$paramcd) || (input$paramcd %in% paramcd_choices)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">152</td>
+                    <td class="num">315</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">        input$paramcd</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">153</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">316</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">154</td>
+                    <td class="num">317</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">        showNotification(type = "warning", paste(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">155</td>
+                    <td class="num">318</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">          "Endpoint", input$paramcd, "not available in this data subset, please",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">156</td>
+                    <td class="num">319</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name</pre>
+                      <pre class="language-r">          "change filter options or select another endpoint"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">157</td>
+                    <td class="num">320</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        ))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">158</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">321</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">        ""</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">322</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">159</td>
+                    <td class="num">323</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r">      updateSelectizeInput(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">160</td>
+                    <td class="num">324</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = experiment$assays,</pre>
+                      <pre class="language-r">        "paramcd",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">161</td>
+                    <td class="num">325</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">        choices = paramcd_choices,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">162</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">326</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        selected = new_selected,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">163</td>
+                    <td class="num">327</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    genes &lt;- geneSpecServer(</pre>
+                      <pre class="language-r">        session = session</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">328</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">164</td>
+                    <td class="num">329</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "genes",</pre>
+                      <pre class="language-r">      session$sendCustomMessage(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">165</td>
+                    <td class="num">330</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      funs = summary_funs,</pre>
+                      <pre class="language-r">        "toggle_dropdown",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">166</td>
+                    <td class="num">331</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices = experiment$genes</pre>
+                      <pre class="language-r">        list(input_id = session$ns("paramcd"), disabled = (length(paramcd_choices) == 0))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">167</td>
+                    <td class="num">332</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">168</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">333</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    subgroups &lt;- sampleVarSpecServer(</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">169</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">334</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "subgroups",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">170</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">335</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r">    # Subset zooming in on a specified endpoint.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">171</td>
+                    <td class="num">336</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = experiment$data,</pre>
+                      <pre class="language-r">    adtte_subset &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">172</td>
+                    <td class="num">337</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      categorical_only = TRUE,</pre>
+                      <pre class="language-r">      endpoint &lt;- input$paramcd</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">173</td>
+                    <td class="num">338</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      explicit_na = TRUE</pre>
+                      <pre class="language-r">      adtte_joined &lt;- adtte_joined()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">174</td>
+                    <td class="num">339</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">175</td>
+                    <td class="num">340</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    adtte &lt;- adtteSpecServer(</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">176</td>
+                    <td class="num">341</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "adtte",</pre>
+                      <pre class="language-r">        endpoint,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">177</td>
+                    <td class="num">342</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">        "please select an endpoint"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">178</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">343</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = adtte_name,</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">179</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">344</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">      # Validate that adtte_data is not empty.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">180</td>
+                    <td class="num">345</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">181</td>
+                    <td class="num">346</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data = subgroups$experiment_data,</pre>
+                      <pre class="language-r">        nrow(adtte_joined) &gt; 0,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">182</td>
+                    <td class="num">347</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r">        "Joined ADTTE is empty - please relax the filter criteria"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">183</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">348</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay = assay,</pre>
+                      <pre class="language-r">      ))</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">349</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">184</td>
+                    <td class="num">350</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes = genes,</pre>
+                      <pre class="language-r">      subset_rows &lt;- adtte_joined[[adtte_vars$paramcd]] == endpoint</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">185</td>
+                    <td class="num">351</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      probs = reactive({</pre>
+                      <pre class="language-r">      result &lt;- adtte_joined[subset_rows, , drop = FALSE]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">186</td>
+                    <td class="num">352</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        input$probs</pre>
+                      <pre class="language-r">      droplevels(result)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">187</td>
+                    <td class="num">353</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      })</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">188</td>
+                    <td class="num">354</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">189</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">355</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    binned_adtte_subset &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">190</td>
+                    <td class="num">356</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    surv_subgroups &lt;- reactive({</pre>
+                      <pre class="language-r">      gene_col &lt;- gene_col()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">191</td>
+                    <td class="num">357</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      binned_adtte &lt;- adtte$binned_adtte_subset()</pre>
+                      <pre class="language-r">      probs &lt;- probs()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">192</td>
+                    <td class="num">358</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      subgroups_var &lt;- subgroups$sample_var()</pre>
+                      <pre class="language-r">      adtte_subset &lt;- adtte_subset()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">193</td>
+                    <td class="num">359</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">194</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      tern::extract_survival_subgroups(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">195</td>
+                    <td class="num">360</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        variables = list(</pre>
+                      <pre class="language-r">      result &lt;- tryCatch(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">196</td>
+                    <td class="num">361</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          tte = adtte_vars$aval,</pre>
+                      <pre class="language-r">        expr = {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">197</td>
+                    <td class="num">362</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          is_event = adtte_vars$is_event,</pre>
+                      <pre class="language-r">          dplyr::mutate(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">198</td>
+                    <td class="num">363</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          arm = adtte$gene_factor,</pre>
+                      <pre class="language-r">            adtte_subset,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">199</td>
+                    <td class="num">364</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          subgroups = subgroups_var</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">200</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">            gene_factor = tern::cut_quantile_bins(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">201</td>
+                    <td class="num">365</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label_all = "All Patients",</pre>
+                      <pre class="language-r">              adtte_subset[, gene_col],</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">202</td>
+                    <td class="num">366</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        data = binned_adtte</pre>
+                      <pre class="language-r">              probs = probs</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">203</td>
+                    <td class="num">367</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">            )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">204</td>
+                    <td class="num">368</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">205</td>
+                    <td class="num">369</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        },</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">206</td>
+                    <td class="num">370</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    result &lt;- reactive({</pre>
+                      <pre class="language-r">        error = function(e) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">207</td>
+                    <td class="num">371</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      surv_subgroups &lt;- surv_subgroups()</pre>
+                      <pre class="language-r">          if (grepl("Contains duplicated values", e)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">208</td>
+                    <td class="num">372</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lyt &lt;- rtables::basic_table()</pre>
+                      <pre class="language-r">            validate(paste(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">209</td>
+                    <td class="num">373</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      time_unit &lt;- adtte$time_unit()</pre>
+                      <pre class="language-r">              "please adjust filters or select (slightly) different quantiles",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">210</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">374</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">              "to avoid duplicate quantiles"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">211</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">375</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tern::tabulate_survival_subgroups(</pre>
+                      <pre class="language-r">            ))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">212</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">376</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        lyt = lyt,</pre>
+                      <pre class="language-r">          } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">213</td>
+                    <td class="num">377</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        df = surv_subgroups,</pre>
+                      <pre class="language-r">            stop(e)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">214</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">378</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        vars = c("n_tot_events", "n", "n_events", "median", "hr", "ci"),</pre>
+                      <pre class="language-r">          }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">215</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">379</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        time_unit = time_unit</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">216</td>
+                    <td class="num">380</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
+                  <tr class="missed">
+                    <td class="num">381</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      result</pre>
+                    </td>
+                  </tr>
                   <tr class="never">
-                    <td class="num">217</td>
+                    <td class="num">382</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">218</td>
+                    <td class="num">383</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">219</td>
+                    <td class="num">384</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    forest_plot &lt;- reactive({</pre>
+                      <pre class="language-r">    time_unit &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">220</td>
+                    <td class="num">385</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result &lt;- result()</pre>
+                      <pre class="language-r">      adtte_subset &lt;- adtte_subset()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">221</td>
+                    <td class="num">386</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tern::g_forest(result)</pre>
+                      <pre class="language-r">      result &lt;- unique(as.character(adtte_subset[[adtte_vars$avalu]]))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">387</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      assert_string(result)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">388</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      result</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">222</td>
+                    <td class="num">389</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">390</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">224</td>
+                    <td class="num">391</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">    list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">225</td>
+                    <td class="num">392</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot",</pre>
+                      <pre class="language-r">      binned_adtte_subset = binned_adtte_subset,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">226</td>
+                    <td class="num">393</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = forest_plot,</pre>
+                      <pre class="language-r">      gene_col = gene_col,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">227</td>
+                    <td class="num">394</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      height = plot_height,</pre>
+                      <pre class="language-r">      gene_factor = "gene_factor",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">228</td>
+                    <td class="num">395</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      width = plot_width</pre>
+                      <pre class="language-r">      time_unit = time_unit</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">229</td>
+                    <td class="num">396</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">230</td>
+                    <td class="num">397</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">231</td>
+                    <td class="num">398</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
+                      <pre class="language-r">}</pre>
+                    </td>
+                  </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/geneSpec.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' Module Input for Gene Signature Specification</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">232</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">233</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">5</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">#' This defines the input for the gene signature specification.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">234</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">235</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Forest Plot")</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">236</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Forest Plot", "header2")</pre>
+                      <pre class="language-r">#' @param funs (named `list`)\cr names of this list will be used for the function</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">237</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">#'   selection drop down menu.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">238</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r">#' @param label_genes (`string`)\cr label for the gene selection.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">239</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                      <pre class="language-r">#' @param label_funs (`string`)\cr label for the function selection.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">240</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Experiment:",</pre>
+                      <pre class="language-r">#' @param label_text_button (`string`)\cr label for the text input button.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">241</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">13</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`experiment-name`,</pre>
+                      <pre class="language-r">#' @param label_lock_button (`string`)\cr label for the lock button.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">242</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">14</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAssay:",</pre>
+                      <pre class="language-r">#' @param label_select_all_button (`string`)\cr label for the selecting all genes button.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">243</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`assay-name`,</pre>
+                      <pre class="language-r">#' @param label_select_none_button (`string`)\cr label for the selecting no genes button.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">244</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nGenes Selected:",</pre>
+                      <pre class="language-r">#' @param max_options (`count`)\cr maximum number of gene options rendering and selected via</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">245</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">17</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste0(genes()$get_gene_labels(), collapse = ", "),</pre>
+                      <pre class="language-r">#'   "Select All".</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">246</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">18</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nGene Summary:",</pre>
+                      <pre class="language-r">#' @param max_selected (`count`)\cr maximum number of genes which can be selected.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">247</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`genes-fun_name`,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">248</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">20</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nEndpoint:",</pre>
+                      <pre class="language-r">#' @return The UI part.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">249</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`adtte-paramcd`,</pre>
+                      <pre class="language-r">#' @seealso [geneSpecServer()] for the module server and a complete example.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">250</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nProbability Cutoff:",</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">251</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">23</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$probs,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">252</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">24</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nSubgroup Variable:",</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">253</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`subgroups-sample_var`</pre>
+                      <pre class="language-r">#' geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">254</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">geneSpecInput &lt;- function(inputId, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">255</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">                          funs,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">256</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">                          label_genes = "Select Gene(s)",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">257</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">                          label_funs = "Select Gene Summary",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">258</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">                          label_text_button = "Enter list of genes",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">259</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">                          label_lock_button = "Lock gene selection (so that it does not get updated when filtering)",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">260</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">                          label_select_all_button = paste0("Select All Genes (first ", max_options, ")"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">                          label_select_none_button = "Select None",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">262</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                          max_options = 200L,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">263</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">35</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">                          max_selected = max_options) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">264</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">36</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">  assert_string(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">265</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">37</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_plot(forest_plot(), dim = pws$dim())</pre>
+                      <pre class="language-r">  assert_list(funs, names = "unique", min.len = 1L)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">266</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">38</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">  assert_string(label_genes)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">267</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">39</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">  assert_string(label_funs)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">268</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">40</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r">  assert_string(label_text_button)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">269</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">41</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">  assert_string(label_lock_button)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">270</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">42</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
+                      <pre class="language-r">  assert_string(label_select_all_button)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">271</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">43</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">  assert_string(label_select_none_button)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">272</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">44</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
+                      <pre class="language-r">  assert_count(max_options, positive = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">273</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">45</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">  assert_count(max_selected, positive = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">274</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">275</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">47</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">276</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">48</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  tagList(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">277</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">49</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    include_css_files(pattern = "*"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">278</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">50</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_forest_tte sample module function.</pre>
+                      <pre class="language-r">    div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">279</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">51</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      class = "row",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">280</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">52</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">281</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">53</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        class = "col-sm-8",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">282</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">54</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r">        tags$label(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">283</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">55</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">          class = "control-label",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">284</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">56</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_forest_tte()</pre>
+                      <pre class="language-r">          label_genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">285</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">286</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_forest_tte &lt;- function() { # nolint</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">287</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">59</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">288</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">60</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">        class = "col-sm-2",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">289</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">61</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">        actionButton(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">290</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">62</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dplyr::mutate(is_event = .data$CNSR == 0)</pre>
+                      <pre class="language-r">          ns("select_none_button"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">291</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">63</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          span(icon("remove-circle", lib = "glyphicon")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">292</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">64</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(</pre>
+                      <pre class="language-r">          title = label_select_none_button,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">293</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">65</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    teal.data::dataset(</pre>
+                      <pre class="language-r">          class = "pull-right list-genes"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">294</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "ADTTE",</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">295</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">67</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte,</pre>
+                      <pre class="language-r">        actionButton(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">296</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">          ns("select_all_button"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">297</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">69</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        dplyr::mutate(is_event = .data$CNSR == 0)"</pre>
+                      <pre class="language-r">          span(icon("ok-circle", lib = "glyphicon")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">298</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">70</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">          title = label_select_all_button,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">299</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">          class = "pull-right list-genes"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">300</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">301</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">302</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">303</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">304</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">74</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = teal::modules(</pre>
+                      <pre class="language-r">      div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">305</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tm_g_forest_tte(</pre>
+                      <pre class="language-r">        class = "col-sm-2",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">306</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = "forest",</pre>
+                      <pre class="language-r">        actionButton(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">307</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        adtte_name = "ADTTE",</pre>
+                      <pre class="language-r">          ns("text_button"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">308</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae_name = "MAE"</pre>
+                      <pre class="language-r">          span(icon("fas fa-font")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">309</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">79</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">          title = label_text_button,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">310</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">          class = "pull-right list-genes"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">311</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">312</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">82</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">        div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">313</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">83</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          class = "pull-right",</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/km.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">84</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for `Kaplan-Meier` Plot</pre>
+                      <pre class="language-r">          title = label_lock_button,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          shinyWidgets::prettyToggle(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">            ns("lock_button"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">4</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">87</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            value = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">88</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This teal module produces a grid style `Kaplan-Meier` plot for data with</pre>
+                      <pre class="language-r">            label_on = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">89</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' `ADaM` structure.</pre>
+                      <pre class="language-r">            label_off = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">90</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            status_on = "default",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">91</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">            status_off = "default",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">92</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            outline = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">93</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">            plain = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">94</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            icon_on = icon("fas fa-lock"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">95</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">            icon_off = icon("fas fa-lock-open"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">96</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            animation = "pulse"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dplyr::mutate(is_event = (.data$CNSR == 0))</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">101</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">102</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(</pre>
+                      <pre class="language-r">      class = "custom-select-input",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">20</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">103</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dataset(</pre>
+                      <pre class="language-r">      selectizeInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">21</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">104</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     "ADTTE",</pre>
+                      <pre class="language-r">        ns("genes"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">105</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     adtte,</pre>
+                      <pre class="language-r">        label = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">        choices = "",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">107</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       dplyr::mutate(is_event = (.data$CNSR == 0))"</pre>
+                      <pre class="language-r">        multiple = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">108</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ),</pre>
+                      <pre class="language-r">        selected = 1,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">26</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">109</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   dataset("MAE", mae)</pre>
+                      <pre class="language-r">        options = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">27</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">110</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">          placeholder = "- Nothing selected -",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">111</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          render = I("{</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">29</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">112</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' modules &lt;- modules(</pre>
+                      <pre class="language-r">          option: function(item, escape) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">30</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">113</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   tm_g_km(</pre>
+                      <pre class="language-r">              return '&lt;div&gt; &lt;span style=\"font-size: inherit;\"&gt;' + item.label + '&lt;/div&gt;' +</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">31</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     label = "kaplan-meier",</pre>
+                      <pre class="language-r">                ' &lt;span style=\"color: #808080; font-size: xx-small;\" &gt;' + item.value + '&lt;/div&gt; &lt;/div&gt;'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">115</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     adtte_name = "ADTTE",</pre>
+                      <pre class="language-r">            }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     mae_name = "MAE"</pre>
+                      <pre class="language-r">          }"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">117</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">          searchField = c("value", "label"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">118</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">          maxOptions = max_options,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">36</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">119</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          maxItems = max_selected</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">121</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">122</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">123</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">    conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">41</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">124</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      condition = "input.genes &amp;&amp; input.genes.length &gt; 1",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">42</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">125</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">      ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">43</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">126</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(ui = app$ui, server = app$server)</pre>
+                      <pre class="language-r">      selectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">44</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">127</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        ns("fun_name"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">45</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">128</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_km &lt;- function(label,</pre>
+                      <pre class="language-r">        label_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">46</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">7<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    adtte_name,</pre>
+                      <pre class="language-r">        names(funs)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    mae_name,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    adtte_vars = list(</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      aval = "AVAL",</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">50</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      is_event = "is_event",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      paramcd = "PARAMCD",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      usubjid = "USUBJID",</pre>
+                      <pre class="language-r">#' Helper Function to Update Gene Selection</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">136</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      avalu = "AVALU"</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">137</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    ),</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">138</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    exclude_assays = "counts",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    summary_funs = list(</pre>
+                      <pre class="language-r">#' This helper function takes the intersection of `selected` and</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      Mean = colMeans,</pre>
+                      <pre class="language-r">#' `choices` for genes and updates the `inputId` accordingly. It then</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">141</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      Median = matrixStats::colMedians,</pre>
+                      <pre class="language-r">#' shows a notification if not all `selected` genes were available.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                      Max = matrixStats::colMaxs</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">143</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    ),</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    pre_output = NULL,</pre>
+                      <pre class="language-r">#' @param session (`ShinySession`)\cr the session object.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    post_output = NULL) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">63</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  logger::log_info("Initializing tm_g_km")</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">64</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">#' @param selected (`character`)\cr currently selected gene IDs.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">65</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">146</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(adtte_name)</pre>
+                      <pre class="language-r">#' @param choices (`data.frame`)\cr containing `id` and `name` columns of the</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">66</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">147</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">#'   new choices.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">67</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">148</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_adtte_vars(adtte_vars)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">68</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">149</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">69</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">150</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_summary_funs(summary_funs)</pre>
+                      <pre class="language-r">h_update_gene_selection &lt;- function(session,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">70</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">151</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">                                    inputId, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">71</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">152</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">                                    selected,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                                    choices) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">73</td>
+                    <td class="num">154</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
+                      <pre class="language-r">  is_new_selected &lt;- selected %in% choices$id</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">74</td>
+                    <td class="num">155</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
+                      <pre class="language-r">  is_removed &lt;- !is_new_selected</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">75</td>
+                    <td class="num">156</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_km,</pre>
+                      <pre class="language-r">  updateSelectizeInput(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">76</td>
+                    <td class="num">157</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">    session = session,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">77</td>
+                    <td class="num">158</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = adtte_name,</pre>
+                      <pre class="language-r">    inputId = inputId,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">78</td>
+                    <td class="num">159</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">    selected = selected[is_new_selected],</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">79</td>
+                    <td class="num">160</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
+                      <pre class="language-r">    choices = stats::setNames(choices$id, choices$name),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">80</td>
+                    <td class="num">161</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays,</pre>
+                      <pre class="language-r">    server = TRUE</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">81</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">162</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">82</td>
+                    <td class="num">163</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">83</td>
+                    <td class="num">164</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_km,</pre>
+                      <pre class="language-r">  n_removed &lt;- sum(is_removed)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">84</td>
+                    <td class="num">165</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">  if (n_removed &gt; 0) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">85</td>
+                    <td class="num">166</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = adtte_name,</pre>
+                      <pre class="language-r">    showNotification(paste(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">86</td>
+                    <td class="num">167</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">      "Removed", n_removed, ifelse(n_removed &gt; 1, "genes", "gene"),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">87</td>
+                    <td class="num">168</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">      hermes::h_parens(hermes::h_short_list(selected[is_removed]))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">88</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">169</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">    ))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">89</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">170</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">90</td>
+                    <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">91</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">172</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = c(adtte_name, mae_name)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">92</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' Helper Function to Parse Genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">93</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">94</td>
+                    <td class="num">175</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">95</td>
+                    <td class="num">176</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_km sets up the user interface.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">96</td>
+                    <td class="num">177</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#' This helper function takes a vector of `words` and tries to match them</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">97</td>
+                    <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' with the `id` and `name` columns of possible gene choices.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">179</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ui_g_km &lt;- function(id,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    data,</pre>
+                      <pre class="language-r">#' @param words (`character`)\cr containing gene IDs or names.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">100</td>
+                    <td class="num">181</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    adtte_name,</pre>
+                      <pre class="language-r">#' @inheritParams h_update_gene_selection</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">101</td>
+                    <td class="num">182</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    mae_name,</pre>
+                      <pre class="language-r">#' @return The subset of `choices` which matches `words` in ID or name.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">102</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    summary_funs,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    pre_output,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                    post_output) {</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">186</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">#' h_parse_genes(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">106</td>
+                    <td class="num">187</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   c("a", "2535"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">107</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">188</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">#'   data.frame(id = as.character(2533:2537), name = letters[1:5])</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">108</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">189</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    encoding = div(</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">190</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ### Reporter</pre>
+                      <pre class="language-r">h_parse_genes &lt;- function(words, choices) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">110</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">191</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_character(words, min.len = 1L)</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">192</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_data_frame(choices, types = "character")</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">193</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">  assert_set_equal(names(choices), c("id", "name"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ###</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">112</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">113</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">195</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r">  id_matches &lt;- choices$id %in% words</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">114</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">196</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r">  name_matches &lt;- choices$name %in% words</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">115</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">197</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r">  has_match &lt;- id_matches | name_matches</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">116</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="num">198</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      geneSpecInput(ns("genes"), summary_funs),</pre>
+                      <pre class="language-r">  choices[has_match, , drop = FALSE]</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">117</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">199</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of ADTTE:", tags$code(adtte_name)),</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">118</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">200</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtteSpecInput(ns("adtte")),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">119</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">201</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::panel_group(</pre>
+                      <pre class="language-r">#' Module Server for Gene Signature Specification</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">120</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">202</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::panel_item(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">121</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">203</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input_id = "settings_item",</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">122</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">204</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          collapsed = TRUE,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">123</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">205</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = "Additional Settings",</pre>
+                      <pre class="language-r">#' This defines the server part for the gene signature specification.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">124</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">206</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("strata"), "Select Strata"),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">125</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">207</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sliderInput(</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">126</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">208</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            ns("percentiles"),</pre>
+                      <pre class="language-r">#' @param funs (static named `list`)\cr names of this list will be used for the function</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">127</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">209</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            "Select quantiles to be displayed",</pre>
+                      <pre class="language-r">#'   selection drop down menu.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">128</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">210</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            min = 0,</pre>
+                      <pre class="language-r">#' @param gene_choices (reactive `data.frame`)\cr returns the possible gene choices to</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">211</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            max = 1,</pre>
+                      <pre class="language-r">#'   populate in the UI, as a `data.frame` with columns `id` and `name`.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">130</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">212</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            value = c(0, 0.5)</pre>
+                      <pre class="language-r">#' @param label_modal_title (`string`)\cr title for the dialog that asks for the text input.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">131</td>
+                    <td class="num">213</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">#' @param label_modal_footer (`character`)\cr lines of text to use for the footer of the dialog.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">132</td>
+                    <td class="num">214</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @return Reactive [`hermes::GeneSpec`] which can be used as input for the relevant</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">134</td>
+                    <td class="num">216</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">#'   `hermes` functions.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">135</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">217</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                      <pre class="language-r">#' @seealso [geneSpecInput()] for the module UI.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">136</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">218</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pre_output = pre_output,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">137</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">219</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    post_output = post_output</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">138</td>
+                    <td class="num">220</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">139</td>
+                    <td class="num">221</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">140</td>
+                    <td class="num">222</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' ui &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_km sets up the user interface.</pre>
+                      <pre class="language-r">#'                data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">224</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'                funs) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">225</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">226</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_km &lt;- function(id,</pre>
+                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">227</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     data,</pre>
+                      <pre class="language-r">#'     encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">146</td>
+                    <td class="num">228</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     filter_panel_api,</pre>
+                      <pre class="language-r">#'       geneSpecInput(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">147</td>
+                    <td class="num">229</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     reporter,</pre>
+                      <pre class="language-r">#'         ns("my_genes"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">148</td>
+                    <td class="num">230</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     adtte_name,</pre>
+                      <pre class="language-r">#'         funs = funs,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">149</td>
+                    <td class="num">231</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     mae_name,</pre>
+                      <pre class="language-r">#'         label_funs = "Please select function"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">150</td>
+                    <td class="num">232</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     adtte_vars,</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">151</td>
+                    <td class="num">233</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     summary_funs,</pre>
+                      <pre class="language-r">#'     ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">152</td>
+                    <td class="num">234</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                     exclude_assays) {</pre>
+                      <pre class="language-r">#'     output = textOutput(ns("result"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">153</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">235</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">154</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">236</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">155</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">237</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">#' server &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">156</td>
+                    <td class="num">238</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'                    data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">157</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">239</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">#'                    funs) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">158</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">240</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">159</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">241</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">#'     gene_choices &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">160</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">242</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">#'       mae &lt;- data[["MAE"]]()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">161</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">243</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">#'       object &lt;- mae[[1]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">162</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">244</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">#'       gene_ids &lt;- rownames(object)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">163</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">245</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sample_vars_as_factors = FALSE # To avoid converting logical `event` to factor.</pre>
+                      <pre class="language-r">#'       gene_names &lt;- SummarizedExperiment::rowData(object)$symbol</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">164</td>
+                    <td class="num">246</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'       gene_data &lt;- data.frame(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">165</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">247</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">#'         id = gene_ids,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">166</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">248</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r">#'         name = gene_names</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">167</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">249</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = experiment$assays,</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">168</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">250</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">#'       gene_data[order(gene_data$name), ]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">169</td>
+                    <td class="num">251</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">170</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">252</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    genes &lt;- geneSpecServer(</pre>
+                      <pre class="language-r">#'     gene_spec &lt;- geneSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">171</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">253</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "genes",</pre>
+                      <pre class="language-r">#'       "my_genes",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">172</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">254</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      funs = summary_funs,</pre>
+                      <pre class="language-r">#'       funs = funs,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">173</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">255</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices = experiment$genes</pre>
+                      <pre class="language-r">#'       gene_choices = gene_choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">174</td>
+                    <td class="num">256</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">175</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">257</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    strata &lt;- sampleVarSpecServer(</pre>
+                      <pre class="language-r">#'     output$result &lt;- renderText({</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">176</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">258</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "strata",</pre>
+                      <pre class="language-r">#'       validate_gene_spec(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">177</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">259</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r">#'         gene_spec(),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">178</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">260</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = experiment$data</pre>
+                      <pre class="language-r">#'         gene_choices()$id</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">179</td>
+                    <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">180</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">262</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    percentiles_without_borders &lt;- reactive({</pre>
+                      <pre class="language-r">#'       gene_spec &lt;- gene_spec()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">181</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">263</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      percentiles &lt;- input$percentiles</pre>
+                      <pre class="language-r">#'       gene_spec$get_label()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">182</td>
+                    <td class="num">264</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">183</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">265</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result &lt;- setdiff(percentiles, c(0, 1))</pre>
+                      <pre class="language-r">#'   })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">184</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">266</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">185</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">267</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        length(result) &gt; 0,</pre>
+                      <pre class="language-r">#' funs &lt;- list(mean = colMeans)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">186</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">268</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Please select at least one quantile other than 0 and 1"</pre>
+                      <pre class="language-r">#' my_app &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">187</td>
+                    <td class="num">269</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">188</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">270</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result</pre>
+                      <pre class="language-r">#'   mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">189</td>
+                    <td class="num">271</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">190</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">272</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    adtte &lt;- adtteSpecServer(</pre>
+                      <pre class="language-r">#'   app &lt;- init(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">191</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">273</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "adtte",</pre>
+                      <pre class="language-r">#'     data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">192</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">274</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">#'     modules = modules(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">193</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">275</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = adtte_name,</pre>
+                      <pre class="language-r">#'       module(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">194</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">276</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">#'         label = "GeneSpec example",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">195</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">277</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
+                      <pre class="language-r">#'         server = server,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">196</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">278</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data = strata$experiment_data,</pre>
+                      <pre class="language-r">#'         server_args = list(funs = funs),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">197</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">279</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r">#'         ui = ui,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">198</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">280</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay = assay,</pre>
+                      <pre class="language-r">#'         ui_args = list(funs = funs),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">199</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">281</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes = genes,</pre>
+                      <pre class="language-r">#'         datanames = "all"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">200</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">282</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      probs = percentiles_without_borders</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">201</td>
+                    <td class="num">283</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">202</td>
+                    <td class="num">284</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">203</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">285</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    km_plot &lt;- reactive({</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">204</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">286</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      strata_var &lt;- strata$sample_var()</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">205</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">287</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      binned_adtte &lt;- adtte$binned_adtte_subset()</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">206</td>
+                    <td class="num">288</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   my_app()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">207</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">289</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      variables &lt;- list(</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">208</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">290</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tte = adtte_vars$aval,</pre>
+                      <pre class="language-r">geneSpecServer &lt;- function(id, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">209</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">291</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is_event = adtte_vars$is_event,</pre>
+                      <pre class="language-r">                           funs,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">210</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">292</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        arm = adtte$gene_factor,</pre>
+                      <pre class="language-r">                           gene_choices,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">211</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">293</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        strat = strata_var</pre>
+                      <pre class="language-r">                           label_modal_title = "Enter list of genes",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">212</td>
+                    <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">                           label_modal_footer = c(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">213</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">295</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tern::g_km(binned_adtte, variables = variables, annot_coxph = TRUE)</pre>
+                      <pre class="language-r">                             "Please enter a comma-separated list of gene IDs and/or names.",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">214</td>
+                    <td class="num">296</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">                             "(Note that genes not included in current choices will be removed)"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">215</td>
+                    <td class="num">297</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                           )) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">216</td>
+                    <td class="num">298</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$km_plot &lt;- renderPlot(km_plot())</pre>
+                      <pre class="language-r">  assert_string(id)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">217</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">299</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_list(funs, names = "unique", min.len = 1L)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">218</td>
+                    <td class="num">300</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">  assert_reactive(gene_choices)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">219</td>
+                    <td class="num">301</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot",</pre>
+                      <pre class="language-r">  assert_string(label_modal_title)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">220</td>
+                    <td class="num">302</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = km_plot</pre>
+                      <pre class="language-r">  assert_character(label_modal_footer)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">221</td>
+                    <td class="num">303</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">304</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">222</td>
+                    <td class="num">305</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # The `reactiveValues` object for storing current gene text input.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">306</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
+                      <pre class="language-r">    # This will also be a data frame with id and name columns.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">224</td>
+                    <td class="num">307</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">    parsed_genes &lt;- reactiveVal(NULL, label = "Parsed genes")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">225</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">308</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">226</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">309</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">    # If the parsed genes are entered via text, update gene selection.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">227</td>
+                    <td class="num">310</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Kaplan-Meier Plot")</pre>
+                      <pre class="language-r">    observeEvent(parsed_genes(), ignoreNULL = TRUE, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">228</td>
+                    <td class="num">311</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Kaplan-Meier Plot", "header2")</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">229</td>
+                    <td class="num">312</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">      parsed_genes &lt;- parsed_genes()</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">313</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">230</td>
+                    <td class="num">314</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r">      h_update_gene_selection(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">231</td>
+                    <td class="num">315</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                      <pre class="language-r">        session,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">232</td>
+                    <td class="num">316</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Experiment:",</pre>
+                      <pre class="language-r">        inputId = "genes",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">233</td>
+                    <td class="num">317</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`experiment-name`,</pre>
+                      <pre class="language-r">        selected = parsed_genes$id,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">234</td>
+                    <td class="num">318</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAssay:",</pre>
+                      <pre class="language-r">        choices = gene_choices</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">235</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">319</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`assay-name`,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">236</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">320</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nGenes Selected:",</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">237</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">321</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste0(genes()$get_gene_labels(), collapse = ", "),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">238</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">322</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nGene Summary:",</pre>
+                      <pre class="language-r">    # When</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">239</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">323</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`genes-fun_name`,</pre>
+                      <pre class="language-r">    # 1) the gene choices are recomputed,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">240</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">324</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nEndpoint:",</pre>
+                      <pre class="language-r">    # 2) the lock is pressed and then switched off,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">241</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">325</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`adtte-paramcd`,</pre>
+                      <pre class="language-r">    # then update gene selection.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">242</td>
+                    <td class="num">326</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nStrata Selected:",</pre>
+                      <pre class="language-r">    observeEvent(list(gene_choices(), input$lock_button), {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">243</td>
+                    <td class="num">327</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`strata-sample_var`,</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">244</td>
+                    <td class="num">328</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nQuantiles Displayed:",</pre>
+                      <pre class="language-r">      lock_button &lt;- input$lock_button</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">245</td>
+                    <td class="num">329</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste0(input$percentiles, collapse = "-")</pre>
+                      <pre class="language-r">      old_selected &lt;- input$genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">246</td>
+                    <td class="num">330</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">247</td>
+                    <td class="num">331</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">      if (isFALSE(lock_button)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">248</td>
+                    <td class="num">332</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">        h_update_gene_selection(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">249</td>
+                    <td class="num">333</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">          session,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">250</td>
+                    <td class="num">334</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">          inputId = "genes",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">251</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">335</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">          selected = old_selected,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">252</td>
+                    <td class="num">336</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">          choices = gene_choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">253</td>
+                    <td class="num">337</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">254</td>
+                    <td class="num">338</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">255</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">339</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">256</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">340</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">257</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">341</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_plot(km_plot(), dim = pws$dim())</pre>
+                      <pre class="language-r">    # When the Select All button is pressed and not locked, select all genes.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">258</td>
+                    <td class="num">342</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">    observeEvent(input$select_all_button, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">259</td>
+                    <td class="num">343</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">260</td>
+                    <td class="num">344</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r">      lock_button &lt;- input$lock_button</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">345</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">262</td>
+                    <td class="num">346</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">263</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">      if (isFALSE(lock_button)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">264</td>
+                    <td class="num">347</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">265</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">        h_update_gene_selection(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">266</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">348</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r">          session,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">267</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">349</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">          inputId = "genes",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">268</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">350</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          selected = gene_choices$id,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">269</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">351</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          choices = gene_choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">270</td>
+                    <td class="num">352</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_km sample module function.</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">353</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">272</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">354</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">        showNotification(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">273</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">355</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "Please unlock if you would like to select all genes",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">274</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">356</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r">          type = "warning"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">275</td>
+                    <td class="num">357</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">276</td>
+                    <td class="num">358</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_km()</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">277</td>
+                    <td class="num">359</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">278</td>
+                    <td class="num">360</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_km &lt;- function() { # nolint</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">279</td>
+                    <td class="num">361</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # When the Select None button is pressed and not locked, select none.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">280</td>
+                    <td class="num">362</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">    observeEvent(input$select_none_button, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">281</td>
+                    <td class="num">363</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">282</td>
+                    <td class="num">364</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dplyr::mutate(is_event = (.data$CNSR == 0))</pre>
+                      <pre class="language-r">      lock_button &lt;- input$lock_button</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">283</td>
+                    <td class="num">365</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">284</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">285</td>
+                    <td class="num">366</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    teal.data::dataset(</pre>
+                      <pre class="language-r">      if (isFALSE(lock_button)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">286</td>
+                    <td class="num">367</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "ADTTE",</pre>
+                      <pre class="language-r">        h_update_gene_selection(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">287</td>
+                    <td class="num">368</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte,</pre>
+                      <pre class="language-r">          session,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">288</td>
+                    <td class="num">369</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
+                      <pre class="language-r">          inputId = "genes",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">289</td>
+                    <td class="num">370</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        dplyr::mutate(is_event = (.data$CNSR == 0))"</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">290</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">          selected = character(),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">291</td>
+                    <td class="num">371</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">          choices = gene_choices</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">292</td>
+                    <td class="num">372</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">293</td>
+                    <td class="num">373</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">294</td>
+                    <td class="num">374</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  modules &lt;- teal::modules(</pre>
+                      <pre class="language-r">        showNotification(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">295</td>
+                    <td class="num">375</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    tm_g_km(</pre>
+                      <pre class="language-r">          "Please unlock if you would like to select none",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">296</td>
+                    <td class="num">376</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      label = "kaplan-meier",</pre>
+                      <pre class="language-r">          type = "warning"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">297</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">377</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      adtte_name = "ADTTE",</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">298</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">378</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = "MAE"</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">299</td>
+                    <td class="num">379</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">300</td>
+                    <td class="num">380</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">301</td>
+                    <td class="num">381</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # Return the UI for a modal dialog with gene text input, showing examples.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">302</td>
+                    <td class="num">382</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                      <pre class="language-r">    dataModal &lt;- function(example_list) { # nolint</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">303</td>
+                    <td class="num">383</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r">      modalDialog(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">304</td>
+                    <td class="num">384</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = modules</pre>
+                      <pre class="language-r">        textInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">305</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">385</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">          session$ns("gene_text"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">306</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">386</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          label = label_modal_title,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">307</td>
+                    <td class="num">387</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(ui = app$ui, server = app$server)</pre>
+                      <pre class="language-r">          placeholder = example_list</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">308</td>
+                    <td class="num">388</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/scatterplot.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">389</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for RNA-seq Scatterplot</pre>
+                      <pre class="language-r">        do.call("span", as.list(label_modal_footer)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">390</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        footer = tagList(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">391</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">          modalButton("Cancel"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">4</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">392</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          actionButton(session$ns("ok_button"), "OK")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">393</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This module provides an interactive scatterplot for RNA-seq gene expression</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">394</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' analysis.</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">395</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">396</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">397</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    # Show modal when the text button is clicked.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">398</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">    observeEvent(input$text_button, {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">399</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">400</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      example_list &lt;- hermes::h_short_list(utils::head(setdiff(gene_choices$name, "")))</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">401</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      showModal(dataModal(example_list))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">402</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">403</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">404</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">    # When OK button is pressed, attempt to parse the genes from the text.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">405</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">    # This can be IDs and/or names of genes.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">406</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">    # Remove the modal and display notification message.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">407</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r">    observeEvent(input$ok_button, {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">408</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">      gene_text &lt;- input$gene_text</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">20</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">409</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules(</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">410</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     tm_g_scatterplot(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">411</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       label = "scatterplot",</pre>
+                      <pre class="language-r">      if (!nzchar(gene_text)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">412</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">        showNotification(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">413</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">          "Please enter at least one full gene ID.",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">414</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">          type = "error"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">415</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">416</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">417</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">        words &lt;- h_extract_words(gene_text)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">29</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">418</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        parse_result &lt;- h_parse_genes(words, choices = gene_choices)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">30</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">419</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_scatterplot &lt;- function(label,</pre>
+                      <pre class="language-r">        showNotification(paste(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">31</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">420</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             mae_name,</pre>
+                      <pre class="language-r">          "Parsed total", nrow(parse_result), "genes from", length(words), "words"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">421</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             exclude_assays = "counts",</pre>
+                      <pre class="language-r">        ))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">33</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">422</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             summary_funs = list(</pre>
+                      <pre class="language-r">        parsed_genes(parse_result)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">423</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                               Mean = colMeans,</pre>
+                      <pre class="language-r">        removeModal()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">424</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                               Median = matrixStats::colMedians,</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">425</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                               Max = matrixStats::colMaxs</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">426</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">427</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             pre_output = NULL,</pre>
+                      <pre class="language-r">    # When the gene choice is updated, then also set the names</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">428</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             post_output = NULL) {</pre>
+                      <pre class="language-r">    # correctly by looking up in current choices.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">40</td>
+                    <td class="num">429</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  logger::log_info("Initializing tm_g_scatterplot")</pre>
+                      <pre class="language-r">    named_genes &lt;- eventReactive(input$genes, ignoreNULL = FALSE, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">41</td>
+                    <td class="num">430</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">      genes &lt;- input$genes</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">42</td>
+                    <td class="num">431</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">43</td>
+                    <td class="num">432</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
+                      <pre class="language-r">      ret &lt;- if (!is.null(genes)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">44</td>
+                    <td class="num">433</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_summary_funs(summary_funs)</pre>
+                      <pre class="language-r">        which_id &lt;- match(genes, gene_choices$id)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">45</td>
+                    <td class="num">434</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">        gene_names &lt;- gene_choices$name[which_id]</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">46</td>
+                    <td class="num">435</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">        stats::setNames(genes, gene_names)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">436</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">48</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">49</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">50</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_scatterplot,</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">51</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">52</td>
+                    <td class="num">437</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">        NULL</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">53</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">438</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">54</td>
+                    <td class="num">439</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">      ret</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">440</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">56</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">441</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_scatterplot,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">57</td>
+                    <td class="num">442</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">    reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">58</td>
+                    <td class="num">443</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">      hermes::gene_spec(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">59</td>
+                    <td class="num">444</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">        genes = named_genes(),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">60</td>
+                    <td class="num">445</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">        fun = funs[[input$fun_name]],</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">61</td>
+                    <td class="num">446</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">        fun_name = input$fun_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">447</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">63</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">448</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = mae_name</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">449</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">450</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">451</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">452</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_scatterplot sets up the user interface.</pre>
+                      <pre class="language-r">#' Validation of Gene Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">453</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">454</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">455</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ui_g_scatterplot &lt;- function(id,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">456</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             data,</pre>
+                      <pre class="language-r">#' This validation function checks that a given [`hermes::GeneSpec`] has at least</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">457</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             mae_name,</pre>
+                      <pre class="language-r">#' one gene selected and that all genes are included in possible choices.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">458</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             summary_funs,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">459</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             pre_output,</pre>
+                      <pre class="language-r">#' @param gene_spec (`GeneSpec`)\cr gene specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">460</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             post_output) {</pre>
+                      <pre class="language-r">#' @param gene_choices (`character`)\cr all possible gene choices.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">76</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">461</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">462</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">463</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  smooth_method_choices &lt;- c(</pre>
+                      <pre class="language-r">validate_gene_spec &lt;- function(gene_spec,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">79</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">464</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    Linear = "lm",</pre>
+                      <pre class="language-r">                               gene_choices) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">80</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">465</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    Loess = "loess",</pre>
+                      <pre class="language-r">  assert_r6(gene_spec, "GeneSpec")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">81</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">466</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    None = "none"</pre>
+                      <pre class="language-r">  assert_character(gene_choices)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">82</td>
+                    <td class="num">467</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">83</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">468</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  validate(need(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">84</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">469</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">    !is.null(gene_spec$get_genes()),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">470</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    encoding = div(</pre>
+                      <pre class="language-r">    "please select at least one gene"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">86</td>
+                    <td class="num">471</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ### Reporter</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">87</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">  ))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">88</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">472</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ###</pre>
+                      <pre class="language-r">  genes_not_included &lt;- setdiff(gene_spec$get_genes(), gene_choices)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">473</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r">  n_not_incl &lt;- length(genes_not_included)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">474</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r">  validate(need(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">91</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">475</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r">    identical(n_not_incl, 0L),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">92</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">476</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r">    paste(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">93</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">477</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      geneSpecInput(ns("x_spec"), summary_funs, label_genes = "Select x Gene(s)"),</pre>
+                      <pre class="language-r">      n_not_incl,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">478</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      geneSpecInput(ns("y_spec"), summary_funs, label_genes = "Select y Gene(s)"),</pre>
+                      <pre class="language-r">      ifelse(n_not_incl &gt; 1, "genes", "gene"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">479</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::panel_group(</pre>
+                      <pre class="language-r">      hermes::h_parens(hermes::h_short_list(genes_not_included)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">96</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">480</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::panel_item(</pre>
+                      <pre class="language-r">      "not included, please unlock or change filters"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">97</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">481</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input_id = "settings_item",</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">98</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">482</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          collapsed = TRUE,</pre>
+                      <pre class="language-r">  ))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">99</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">483</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = "Additional Settings",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">100</td>
-                    <td class="coverage">1<em>x</em></td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/volcanoplot.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("color_var"), "Optional color variable"),</pre>
+                      <pre class="language-r">#' Teal Module for RNA-seq Volcano Plot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">101</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("facet_var"), "Optional facet variable"),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">102</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selectInput(ns("smooth_method"), "Select smoother", smooth_method_choices)</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' This module provides an interactive volcano plot for RNA-seq gene expression</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">#' analysis.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">107</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pre_output = pre_output,</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">108</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    post_output = post_output</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_scatterplot sets up the server with reactive graph.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">113</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">114</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">115</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_scatterplot &lt;- function(id,</pre>
+                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              data,</pre>
+                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">117</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              filter_panel_api,</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              reporter,</pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">119</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              mae_name,</pre>
+                      <pre class="language-r">#'   modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">120</td>
+                    <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              exclude_assays,</pre>
+                      <pre class="language-r">#'     tm_g_volcanoplot(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                              summary_funs) {</pre>
+                      <pre class="language-r">#'       label = "volcanoplot",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">122</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">23</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">123</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">24</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">124</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">126</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">127</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">128</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">129</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">tm_g_volcanoplot &lt;- function(label,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">130</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">31</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">                             mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">131</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name</pre>
+                      <pre class="language-r">                             exclude_assays = character(),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">132</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                             pre_output = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">133</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">                             post_output = NULL) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">134</td>
+                    <td class="num">35</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r">  logger::log_info("Initializing tm_g_volcanoplot")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">135</td>
+                    <td class="num">36</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = experiment$assays,</pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">136</td>
+                    <td class="num">37</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">137</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">38</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">  assert_character(exclude_assays)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">138</td>
+                    <td class="num">39</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    sample_var_specs &lt;- multiSampleVarSpecServer(</pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">139</td>
+                    <td class="num">40</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      inputIds = c("facet_var", "color_var"),</pre>
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">140</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">41</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">141</td>
+                    <td class="num">42</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = experiment$data</pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">142</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">43</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">143</td>
+                    <td class="num">44</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x_spec &lt;- geneSpecServer("x_spec", summary_funs, experiment$genes)</pre>
+                      <pre class="language-r">    server = srv_g_volcanoplot,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">144</td>
+                    <td class="num">45</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    y_spec &lt;- geneSpecServer("y_spec", summary_funs, experiment$genes)</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">145</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">46</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">146</td>
+                    <td class="num">47</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">147</td>
+                    <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Resolve all reactivity.</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">148</td>
+                    <td class="num">49</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- sample_var_specs$experiment_data()</pre>
+                      <pre class="language-r">    ui = ui_g_volcanoplot,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">149</td>
+                    <td class="num">50</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      x_spec &lt;- x_spec()</pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">150</td>
+                    <td class="num">51</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      y_spec &lt;- y_spec()</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">151</td>
+                    <td class="num">52</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      facet_var &lt;- sample_var_specs$vars$facet_var()</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">152</td>
+                    <td class="num">53</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      color_var &lt;- sample_var_specs$vars$color_var()</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">153</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">54</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay_name &lt;- assay()</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">154</td>
+                    <td class="num">55</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      smooth_method &lt;- input$smooth_method</pre>
+                      <pre class="language-r">    datanames = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">155</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">156</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">57</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate_gene_spec(x_spec, rownames(experiment_data))</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">157</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">58</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate_gene_spec(y_spec, rownames(experiment_data))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">158</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @describeIn tm_g_volcanoplot sets up the user interface.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">159</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Require which states need to be truthy.</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">160</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">61</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">161</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">62</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        smooth_method,</pre>
+                      <pre class="language-r">ui_g_volcanoplot &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        # Note: The following statements are important to make sure the UI inputs have been updated.</pre>
+                      <pre class="language-r">                             data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">163</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        isTRUE(assay_name %in% SummarizedExperiment::assayNames(experiment_data)),</pre>
+                      <pre class="language-r">                             mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">164</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">65</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is.null(facet_var) || isTRUE(facet_var %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                      <pre class="language-r">                             pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">165</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is.null(color_var) || isTRUE(color_var %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                      <pre class="language-r">                             post_output) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">166</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">67</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cancelOutput = FALSE</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">167</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">  mae &lt;- data[[mae_name]]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">168</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">169</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">70</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::draw_scatterplot(</pre>
+                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">170</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object = experiment_data,</pre>
+                      <pre class="language-r">    output = div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">171</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">72</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay_name = assay_name,</pre>
+                      <pre class="language-r">      teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">172</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">73</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        x_spec = x_spec,</pre>
+                      <pre class="language-r">      DT::DTOutput(ns("table"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">173</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        y_spec = y_spec,</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">174</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        facet_var = facet_var,</pre>
+                      <pre class="language-r">    pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">175</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        color_var = color_var,</pre>
+                      <pre class="language-r">    post_output = post_output,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">176</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        smooth_method = smooth_method</pre>
+                      <pre class="language-r">    encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">177</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">      ### Reporter</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">178</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">79</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">179</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">80</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
+                      <pre class="language-r">      ###</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">180</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">81</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">181</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">82</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">182</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">83</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot",</pre>
+                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">183</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">84</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = plot_r</pre>
+                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">184</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      sampleVarSpecInput(ns("compare_group"), "Compare Groups", "Please group here into 2 levels"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">185</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      tags$label("Show Top Differentiated Genes"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">186</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">87</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
+                      <pre class="language-r">      shinyWidgets::switchInput(ns("show_top_gene"), value = FALSE, size = "mini"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">187</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">88</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">      teal.widgets::panel_group(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">188</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">89</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">        teal.widgets::panel_item(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">189</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">90</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">          input_id = "settings_item",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">190</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">91</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Scatter Plot")</pre>
+                      <pre class="language-r">          collapsed = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">191</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">92</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Scatter Plot", "header2")</pre>
+                      <pre class="language-r">          title = "Additional Settings",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">192</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">93</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">          selectInput(ns("method"), "Method", choices = c("voom", "deseq2")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">193</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">94</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r">          sliderInput(ns("log2_fc_thresh"), "Log2 fold change threshold", value = 2.5, min = 0.1, max = 10),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">194</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">95</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                      <pre class="language-r">          sliderInput(ns("adj_p_val_thresh"), "Adjusted p-value threshold", value = 0.05, min = 0.001, max = 1)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">195</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">96</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Experiment:",</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">196</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">97</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`experiment-name`,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">197</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">98</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAssay:",</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">198</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">99</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`assay-name`,</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">199</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">100</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nX Genes Selected:",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">200</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">101</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste0(x_spec()$get_gene_labels(), collapse = ", "),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">201</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">102</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nX Genes Summary:",</pre>
+                      <pre class="language-r">#' @describeIn tm_g_volcanoplot sets up the server with reactive graph.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">202</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">103</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`x_spec-fun_name`,</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">203</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">104</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nY Genes Selected:",</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">204</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">105</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste0(y_spec()$get_gene_labels(), collapse = ", "),</pre>
+                      <pre class="language-r">srv_g_volcanoplot &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">205</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">106</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nY Genes Summary:",</pre>
+                      <pre class="language-r">                              data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">206</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">107</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`y_spec-fun_name`,</pre>
+                      <pre class="language-r">                              filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">207</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">108</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nOptional Color Variable:",</pre>
+                      <pre class="language-r">                              reporter,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">208</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">109</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`color_var-sample_var`,</pre>
+                      <pre class="language-r">                              mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">209</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">110</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nOptional Facetting Variable:",</pre>
+                      <pre class="language-r">                              exclude_assays) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">210</td>
+                    <td class="num">111</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`facet_var-sample_var`,</pre>
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">211</td>
+                    <td class="num">112</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nSmoother:",</pre>
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">212</td>
+                    <td class="num">113</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$smooth_method</pre>
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">213</td>
+                    <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">214</td>
+                    <td class="num">115</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">215</td>
+                    <td class="num">116</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">    experiment_data &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">216</td>
+                    <td class="num">117</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">217</td>
+                    <td class="num">118</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">218</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">219</td>
+                    <td class="num">119</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">220</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">      mae_name = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">221</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">222</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">223</td>
+                    <td class="num">121</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">224</td>
+                    <td class="num">122</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">225</td>
+                    <td class="num">123</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">      assays = experiment_data$assays,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">226</td>
+                    <td class="num">124</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">125</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">227</td>
+                    <td class="num">126</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r">    compare_group &lt;- sampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">228</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">127</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">      "compare_group",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">229</td>
+                    <td class="num">128</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
+                      <pre class="language-r">      experiment_name = experiment_data$name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">230</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">129</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">      original_data = experiment_data$data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">231</td>
+                    <td class="num">130</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
+                      <pre class="language-r">      num_levels = 2L,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">232</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">131</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">      label_modal_title = "Please click to group into exactly 2 levels, first level is reference"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">233</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">234</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">235</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    # When the filtered data set or the chosen experiment changes, update</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">236</td>
+                    <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # the differential expression results.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">237</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">136</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_scatterplot sample module function.</pre>
+                      <pre class="language-r">    diff_expr &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">238</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">137</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      object &lt;- compare_group$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">239</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">138</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      compare_group &lt;- compare_group$sample_var()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">240</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">139</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      method &lt;- input$method</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">241</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">242</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">141</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">      req(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">243</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">142</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_scatterplot()</pre>
+                      <pre class="language-r">        object,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">244</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">143</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        method</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">245</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_scatterplot &lt;- function() {</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">246</td>
+                    <td class="num">145</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">247</td>
+                    <td class="num">146</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">        !is.null(compare_group),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">248</td>
+                    <td class="num">147</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
+                      <pre class="language-r">        "Please select a group variable"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">249</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">148</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">250</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">149</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">251</td>
+                    <td class="num">150</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = teal::modules(</pre>
+                      <pre class="language-r">      hermes::diff_expression(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">252</td>
+                    <td class="num">151</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tm_g_scatterplot(</pre>
+                      <pre class="language-r">        object,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">253</td>
+                    <td class="num">152</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = "scatterplot",</pre>
+                      <pre class="language-r">        group = compare_group,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">254</td>
+                    <td class="num">153</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae_name = "MAE"</pre>
+                      <pre class="language-r">        method = method</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">255</td>
+                    <td class="num">154</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">256</td>
+                    <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">257</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">258</td>
+                    <td class="num">157</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">259</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">158</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      diff_expr_result &lt;- diff_expr()</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/sampleVarSpec.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">159</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Input for Sample Variable Specification</pre>
+                      <pre class="language-r">      log2_fc_thresh &lt;- input$log2_fc_thresh</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">160</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      adj_p_val_thresh &lt;- input$adj_p_val_thresh</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">162</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      req(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">163</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        log2_fc_thresh,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">164</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        adj_p_val_thresh</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">165</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the input for the sample variable specification.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">167</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      hermes::autoplot(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">168</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">        diff_expr_result,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">169</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_vars (`string`)\cr label for the sample variable selection.</pre>
+                      <pre class="language-r">        adj_p_val_thresh = adj_p_val_thresh,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">170</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_levels_button (`string`)\cr label for the levels combination button.</pre>
+                      <pre class="language-r">        log2_fc_thresh = log2_fc_thresh</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The UI part.</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">173</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [sampleVarSpecServer()] for the module server and a complete example.</pre>
+                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">175</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    pws_p &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">176</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      id = "plot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">177</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")</pre>
+                      <pre class="language-r">      plot_r = plot_r</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sampleVarSpecInput &lt;- function(inputId, # nolint</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">18</td>
+                    <td class="num">179</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                               label_vars = "Select sample variable",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">19</td>
+                    <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                               label_levels_button = "Combine factor levels") {</pre>
+                      <pre class="language-r">    # Display top genes if switched on.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">20</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">181</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(inputId)</pre>
+                      <pre class="language-r">    show_top_gene_diffexpr &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">21</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">182</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_vars)</pre>
+                      <pre class="language-r">      if (input$show_top_gene) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">22</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">183</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_levels_button)</pre>
+                      <pre class="language-r">        result &lt;- diff_expr()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">184</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        with(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">24</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">185</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
+                      <pre class="language-r">          result,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">25</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">186</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tagList(</pre>
+                      <pre class="language-r">          data.frame(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">26</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">187</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    include_css_files(pattern = "*"),</pre>
+                      <pre class="language-r">            log2_fc = round(log2_fc, 2),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">27</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">188</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    div(</pre>
+                      <pre class="language-r">            stat = round(stat, 2),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">28</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">189</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      class = "row",</pre>
+                      <pre class="language-r">            p_val = format.pval(p_val),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">29</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">190</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      div(</pre>
+                      <pre class="language-r">            adj_p_val = format.pval(adj_p_val),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">30</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">191</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        class = "col-sm-8",</pre>
+                      <pre class="language-r">            row.names = rownames(result)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">31</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">192</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tags$label(</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">32</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">193</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "control-label",</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">33</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">194</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          label_vars</pre>
+                      <pre class="language-r">      } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">195</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">196</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">36</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">198</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      div(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">37</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">199</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        class = "col-sm-4",</pre>
+                      <pre class="language-r">    output$table &lt;- DT::renderDT({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">38</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">200</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        actionButton(</pre>
+                      <pre class="language-r">      DT::datatable(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">39</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">201</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns("levels_button"),</pre>
+                      <pre class="language-r">        show_top_gene_diffexpr(),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">40</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">202</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          span(icon("fas fa-table")),</pre>
+                      <pre class="language-r">        rownames = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">41</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">203</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = label_levels_button,</pre>
+                      <pre class="language-r">        options = list(scrollX = TRUE, pageLength = 30, lengthMenu = c(5, 15, 30, 100)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">42</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">204</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "pull-right list-genes"</pre>
+                      <pre class="language-r">        caption = "Top Differentiated Genes"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">207</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">46</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">208</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    div(</pre>
+                      <pre class="language-r">    ### REPORTER</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">47</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">209</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      class = "custom-select-input",</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">48</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">210</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::optionalSelectInput(</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">49</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">211</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns("sample_var"),</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">50</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">212</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = NULL,</pre>
+                      <pre class="language-r">          title = "Volcano Plot",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">51</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">213</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = "",</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">52</td>
-                    <td class="coverage">4<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">214</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        multiple = FALSE</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">53</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">215</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">216</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">55</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">217</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">56</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">218</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">        encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">57</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">219</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          "Experiment:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">58</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">220</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function For Group List Creation</pre>
+                      <pre class="language-r">          input$`experiment-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">59</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">221</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "\nAssay:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">60</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">222</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">          input$`assay-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">61</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">223</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "\nCompare Groups:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">62</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">224</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This helper function takes an assignment list and converts it to a</pre>
+                      <pre class="language-r">          input$`compare_group-sample_var`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">63</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">225</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' group list.</pre>
+                      <pre class="language-r">          "\nShow Top Differentiated Genes:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">64</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">226</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          input$show_top_gene,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">65</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">227</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x (named `list` of `character`)\cr input assignment list.</pre>
+                      <pre class="language-r">          "\nMethod:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">66</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">228</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return A combination list.</pre>
+                      <pre class="language-r">          input$method,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">67</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">229</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "\nLog2fold Change Threshold:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">68</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">230</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">          input$log2_fc_thresh,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">69</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">231</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "\nAdjusted P-value Threshold:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">70</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">232</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">          input$adj_p_val_thresh</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">233</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' assign_list &lt;- list(</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">72</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">234</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "ASIAN" = "1",</pre>
+                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">73</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">235</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "BLACK OR AFRICAN AMERICAN" = "1",</pre>
+                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">74</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">236</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "MULTIPLE" = "2",</pre>
+                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">75</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">237</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "UNKNOWN" = "2",</pre>
+                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">238</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "WHITE" = "4"</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">77</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">239</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">78</td>
+                    <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' objective_list &lt;- list(</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">241</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "ASIAN/BLACK OR AFRICAN AMERICAN" = c("ASIAN", "BLACK OR AFRICAN AMERICAN"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">80</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">242</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "MULTIPLE/UNKNOWN" = c("MULTIPLE", "UNKNOWN"),</pre>
+                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">81</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">243</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "WHITE" = "WHITE"</pre>
+                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">82</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">244</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws_p$dim())</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">83</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">245</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' result_list &lt;- h_assign_to_group_list(assign_list)</pre>
+                      <pre class="language-r">        if (isTRUE(input$show_top_gene)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">84</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">246</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' stopifnot(identical(result_list, objective_list))</pre>
+                      <pre class="language-r">          card$append_text("Table", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">85</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">247</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_assign_to_group_list &lt;- function(x) {</pre>
+                      <pre class="language-r">          card$append_table(show_top_gene_diffexpr())</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">248</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_list(</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">87</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">249</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x,</pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">88</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">250</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    types = "character",</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">251</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    any.missing = FALSE,</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">252</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    names = "unique",</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">91</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">253</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    unique = FALSE</pre>
+                      <pre class="language-r">        card</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">92</td>
+                    <td class="num">254</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">93</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">255</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  x_vec &lt;- unlist(x)</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">256</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  x_split &lt;- split(names(x_vec), x_vec)</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">257</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  new_levels &lt;- sapply(x_split, hermes::h_short_list, sep = "/")</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">96</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">258</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  stats::setNames(x_split, new_levels)</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">97</td>
+                    <td class="num">259</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">260</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function for Collapsing of Factor Levels</pre>
+                      <pre class="language-r">#' @describeIn tm_g_volcanoplot sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">100</td>
+                    <td class="num">262</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">101</td>
+                    <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">102</td>
+                    <td class="num">264</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">265</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Given a group list and a factor, this helper function collapses the</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">266</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' levels in the factor accordingly and also ensures that the resulting</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">267</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' levels are in the order given in the group list.</pre>
+                      <pre class="language-r">#'   sample_tm_g_volcanoplot()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">106</td>
+                    <td class="num">268</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">269</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x (`factor`)\cr original factor.</pre>
+                      <pre class="language-r">sample_tm_g_volcanoplot &lt;- function() {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">108</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">270</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param group_list (named `list` of `character`)\cr includes the collapsing</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">109</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">271</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   specification.</pre>
+                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">272</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">273</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">274</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    data = data,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">275</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    modules = teal::modules(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">276</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      tm_g_volcanoplot(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">277</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        label = "volcanoplot",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">278</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">279</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">280</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The transformed factor `x` with new levels.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">281</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">113</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">282</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">114</td>
+                    <td class="num">283</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/sampleVarSpec.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">115</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' set.seed(123)</pre>
+                      <pre class="language-r">#' Module Input for Sample Variable Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' x &lt;- factor(sample(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">117</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   size = 30L,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">119</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   replace = TRUE</pre>
+                      <pre class="language-r">#' This defines the input for the sample variable specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">120</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ))</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' group_list &lt;- list(</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "ASIAN/BLACK OR AFRICAN AMERICAN" = c("ASIAN", "BLACK OR AFRICAN AMERICAN"),</pre>
+                      <pre class="language-r">#' @param label_vars (`string`)\cr label for the sample variable selection.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">123</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "MULTIPLE/UNKNOWN" = c("MULTIPLE", "UNKNOWN"),</pre>
+                      <pre class="language-r">#' @param label_levels_button (`string`)\cr label for the levels combination button.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">124</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "WHITE" = "WHITE"</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">#' @return The UI part.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' x_collapsed &lt;- h_collapse_levels(x, group_list)</pre>
+                      <pre class="language-r">#' @seealso [sampleVarSpecServer()] for the module server and a complete example.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">127</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' stopifnot(identical(levels(x_collapsed), names(group_list)))</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">128</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_collapse_levels &lt;- function(x, group_list) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">3<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_factor(x)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">130</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_list(group_list, names = "unique", types = "character")</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">131</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  x_collapsed &lt;- do.call(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">132</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    forcats::fct_collapse,</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">133</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    args = c(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">134</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      list(.f = x),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">135</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      group_list</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">136</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">138</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  factor(x_collapsed, levels = names(group_list))</pre>
+                      <pre class="language-r">#' sampleVarSpecInput("my_vars", label_vars = "Select faceting variable")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">139</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">sampleVarSpecInput &lt;- function(inputId, # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">140</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                               label_vars = "Select sample variable",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Validation of Number of Levels</pre>
+                      <pre class="language-r">                               label_levels_button = "Combine factor levels") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">142</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">20</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  assert_string(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">143</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">21</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">  assert_string(label_vars)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">144</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">22</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  assert_string(label_levels_button)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This validation function checks that a given vector `x` is a factor with</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">146</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">24</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' the specified number of levels.</pre>
+                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">147</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">25</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  tagList(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">148</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">26</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x (`factor`)\cr factor to validate.</pre>
+                      <pre class="language-r">    include_css_files(pattern = "*"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">149</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">27</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param name (`string`)\cr name of `x` in the app.</pre>
+                      <pre class="language-r">    div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">150</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">28</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param n_levels (`count`)\cr required number of factor levels in `x`.</pre>
+                      <pre class="language-r">      class = "row",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">151</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">29</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">152</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">30</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">        class = "col-sm-8",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">153</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">31</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">validate_n_levels &lt;- function(x, name, n_levels) {</pre>
+                      <pre class="language-r">        tags$label(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">154</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">32</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  validate(need(</pre>
+                      <pre class="language-r">          class = "control-label",</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">155</td>
-                    <td class="coverage">3<em>x</em></td>
+                    <td class="num">33</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    is.factor(x),</pre>
+                      <pre class="language-r">          label_vars</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">156</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paste("Variable", name, "is not a factor but a", class(x))</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">157</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ))</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">158</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">36</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(name, min.chars = 1L)</pre>
+                      <pre class="language-r">      div(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">159</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">37</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_count(n_levels, positive = TRUE)</pre>
+                      <pre class="language-r">        class = "col-sm-4",</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">160</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">38</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  validate(need(</pre>
+                      <pre class="language-r">        actionButton(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">161</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">39</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    identical(n_levels, nlevels(x)),</pre>
+                      <pre class="language-r">          ns("levels_button"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">162</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">40</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paste(</pre>
+                      <pre class="language-r">          span(icon("fas fa-table")),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">163</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">41</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Please combine the original levels of", name,</pre>
+                      <pre class="language-r">          title = label_levels_button,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">164</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">42</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "into exactly", n_levels, "levels"</pre>
+                      <pre class="language-r">          class = "pull-right list-genes"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">165</td>
+                    <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">166</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ))</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">167</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">168</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">46</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">169</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">47</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Server for Sample Variable Specification</pre>
+                      <pre class="language-r">      class = "custom-select-input",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">170</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">48</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      teal.widgets::optionalSelectInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">171</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">49</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">        ns("sample_var"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">172</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">50</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        label = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">173</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">51</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the server part for the sample variable specification.</pre>
+                      <pre class="language-r">        choices = "",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">174</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">52</td>
+                    <td class="coverage">4<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        multiple = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">175</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">176</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param experiment_name (reactive `string`)\cr name of the input experiment.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">177</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param original_data (reactive `SummarizedExperiment`)\cr input experiment where the</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">178</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample variables extracted via [SummarizedExperiment::colData()] should be eligible for</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">179</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   selection.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">180</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param transformed_data (reactive `SummarizedExperiment`)\cr used when multiple sample</pre>
+                      <pre class="language-r">#' Helper Function For Group List Creation</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">181</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   variables can be selected in the app. In that case, pass here the pre-transformed data.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">182</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param assign_lists (`reactivevalues`)\cr object to share factor level groupings across multiple</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">183</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample variables.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">184</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param num_levels (`count` or `NULL`)\cr required number of levels after combining original levels.</pre>
+                      <pre class="language-r">#' This helper function takes an assignment list and converts it to a</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">185</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   If `NULL` then all numbers of levels are allowed.</pre>
+                      <pre class="language-r">#' group list.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">186</td>
+                    <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param categorical_only (`flag`)\cr whether only categorical variables should be selected</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">187</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   from.</pre>
+                      <pre class="language-r">#' @param x (named `list` of `character`)\cr input assignment list.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">188</td>
+                    <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param explicit_na (`flag`)\cr whether the `colData` of `original_data` will be transformed with</pre>
+                      <pre class="language-r">#' @return A combination list.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">189</td>
+                    <td class="num">67</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   [hermes::h_df_factors_with_explicit_na] before further processing. That means also that</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">190</td>
+                    <td class="num">68</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `NA` will be made an explicit factor level and counted for `num_levels`.</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">191</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_modal_title (`string`)\cr title for the dialog that asks for the text input.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">192</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">193</td>
+                    <td class="num">71</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Reactive [`SummarizedExperiment::SummarizedExperiment`] which can be used as</pre>
+                      <pre class="language-r">#' assign_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">194</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   input for the relevant `hermes` functions.</pre>
+                      <pre class="language-r">#'   "ASIAN" = "1",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">195</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [sampleVarSpecInput()] for the module UI.</pre>
+                      <pre class="language-r">#'   "BLACK OR AFRICAN AMERICAN" = "1",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">196</td>
+                    <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   "MULTIPLE" = "2",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">197</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @note Only atomic columns (e.g. not `DataFrame` columns) of the `colData`</pre>
+                      <pre class="language-r">#'   "UNKNOWN" = "2",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">198</td>
+                    <td class="num">76</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   which are not completely missing (`NA`) will be shown for selection.</pre>
+                      <pre class="language-r">#'   "WHITE" = "4"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">199</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   If `num_levels` is specified then only factor columns will be available.</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">200</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' objective_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">201</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'   "ASIAN/BLACK OR AFRICAN AMERICAN" = c("ASIAN", "BLACK OR AFRICAN AMERICAN"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">202</td>
+                    <td class="num">80</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   "MULTIPLE/UNKNOWN" = c("MULTIPLE", "UNKNOWN"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">203</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#'   "WHITE" = "WHITE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">204</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ui &lt;- function(id,</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">205</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                data) {</pre>
+                      <pre class="language-r">#' result_list &lt;- h_assign_to_group_list(assign_list)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">206</td>
+                    <td class="num">84</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
+                      <pre class="language-r">#' stopifnot(identical(result_list, objective_list))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">207</td>
+                    <td class="num">85</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae &lt;- data[["MAE"]]()</pre>
+                      <pre class="language-r">h_assign_to_group_list &lt;- function(x) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">208</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   experiment_name_choices &lt;- names(mae)</pre>
+                      <pre class="language-r">  assert_list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">209</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">87</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">    x,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">210</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">88</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     encoding = div(</pre>
+                      <pre class="language-r">    types = "character",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">211</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">89</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       selectInput(ns("experiment_name"), "Select experiment", experiment_name_choices),</pre>
+                      <pre class="language-r">    any.missing = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">212</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">90</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       sampleVarSpecInput(ns("facet_var"), "Select faceting variable")</pre>
+                      <pre class="language-r">    names = "unique",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">213</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">91</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     ),</pre>
+                      <pre class="language-r">    unique = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">214</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output = plotOutput(ns("plot"))</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">215</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">93</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">  x_vec &lt;- unlist(x)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">216</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">94</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">  x_split &lt;- split(names(x_vec), x_vec)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">217</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">95</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' server &lt;- function(id,</pre>
+                      <pre class="language-r">  new_levels &lt;- sapply(x_split, hermes::h_short_list, sep = "/")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">218</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">96</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                    data) {</pre>
+                      <pre class="language-r">  stats::setNames(x_split, new_levels)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">219</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">220</td>
+                    <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     experiment_data &lt;- reactive({</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">221</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       req(input$experiment_name)</pre>
+                      <pre class="language-r">#' Helper Function for Collapsing of Factor Levels</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">222</td>
+                    <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae &lt;- data[["MAE"]]()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       object &lt;- mae[[input$experiment_name]]</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">224</td>
+                    <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       SummarizedExperiment::colData(object) &lt;-</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">225</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         hermes::df_cols_to_factor(SummarizedExperiment::colData(object))</pre>
+                      <pre class="language-r">#' Given a group list and a factor, this helper function collapses the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">226</td>
+                    <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       object</pre>
+                      <pre class="language-r">#' levels in the factor accordingly and also ensures that the resulting</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">227</td>
+                    <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">#' levels are in the order given in the group list.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">228</td>
+                    <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     facet_var_spec &lt;- sampleVarSpecServer(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">229</td>
+                    <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "facet_var",</pre>
+                      <pre class="language-r">#' @param x (`factor`)\cr original factor.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">230</td>
+                    <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experiment_name = reactive({</pre>
+                      <pre class="language-r">#' @param group_list (named `list` of `character`)\cr includes the collapsing</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">231</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         input$experiment_name</pre>
+                      <pre class="language-r">#'   specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">232</td>
+                    <td class="num">110</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       }),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">233</td>
+                    <td class="num">111</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       original_data = experiment_data</pre>
+                      <pre class="language-r">#' @return The transformed factor `x` with new levels.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">234</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">235</td>
+                    <td class="num">113</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output$plot &lt;- renderPlot({</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">236</td>
+                    <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experiment_data_final &lt;- facet_var_spec$experiment_data()</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">237</td>
+                    <td class="num">115</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       facet_var &lt;- facet_var_spec$sample_var()</pre>
+                      <pre class="language-r">#' set.seed(123)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">238</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       hermes::draw_boxplot(</pre>
+                      <pre class="language-r">#' x &lt;- factor(sample(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">239</td>
+                    <td class="num">117</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         experiment_data_final,</pre>
+                      <pre class="language-r">#'   c("ASIAN", "BLACK OR AFRICAN AMERICAN", "MULTIPLE", "UNKNOWN", "WHITE"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">240</td>
+                    <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         assay_name = "counts",</pre>
+                      <pre class="language-r">#'   size = 30L,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">241</td>
+                    <td class="num">119</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         genes = hermes::gene_spec(hermes::genes(experiment_data_final)[1]),</pre>
+                      <pre class="language-r">#'   replace = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">242</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         facet_var = facet_var</pre>
+                      <pre class="language-r">#' ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">243</td>
+                    <td class="num">121</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">#' group_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">244</td>
+                    <td class="num">122</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">#'   "ASIAN/BLACK OR AFRICAN AMERICAN" = c("ASIAN", "BLACK OR AFRICAN AMERICAN"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">245</td>
+                    <td class="num">123</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   })</pre>
+                      <pre class="language-r">#'   "MULTIPLE/UNKNOWN" = c("MULTIPLE", "UNKNOWN"),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">246</td>
+                    <td class="num">124</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#'   "WHITE" = "WHITE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">247</td>
+                    <td class="num">125</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' my_app &lt;- function() {</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">248</td>
+                    <td class="num">126</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">#' x_collapsed &lt;- h_collapse_levels(x, group_list)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">249</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">#' stopifnot(identical(levels(x_collapsed), names(group_list)))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">250</td>
+                    <td class="num">128</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">h_collapse_levels &lt;- function(x, group_list) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">251</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   app &lt;- init(</pre>
+                      <pre class="language-r">  assert_factor(x)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">252</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">130</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     data = data,</pre>
+                      <pre class="language-r">  assert_list(group_list, names = "unique", types = "character")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">253</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">131</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     modules = modules(</pre>
+                      <pre class="language-r">  x_collapsed &lt;- do.call(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">254</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">132</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       module(</pre>
+                      <pre class="language-r">    forcats::fct_collapse,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">255</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">133</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label = "sampleVarSpec example",</pre>
+                      <pre class="language-r">    args = c(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">256</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">134</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server = server,</pre>
+                      <pre class="language-r">      list(.f = x),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">257</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">135</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui = ui,</pre>
+                      <pre class="language-r">      group_list</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">258</td>
+                    <td class="num">136</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         datanames = "all"</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">259</td>
+                    <td class="num">137</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">260</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">138</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">  factor(x_collapsed, levels = names(group_list))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">262</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">263</td>
+                    <td class="num">141</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' Validation of Number of Levels</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">264</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">265</td>
+                    <td class="num">143</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   my_app()</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">266</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">267</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sampleVarSpecServer &lt;- function(id, # nolint</pre>
+                      <pre class="language-r">#' This validation function checks that a given vector `x` is a factor with</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">268</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                experiment_name,</pre>
+                      <pre class="language-r">#' the specified number of levels.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">269</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                original_data,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">270</td>
+                    <td class="num">148</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                transformed_data = original_data,</pre>
+                      <pre class="language-r">#' @param x (`factor`)\cr factor to validate.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">149</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                assign_lists = reactiveValues(),</pre>
+                      <pre class="language-r">#' @param name (`string`)\cr name of `x` in the app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">272</td>
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                num_levels = NULL,</pre>
+                      <pre class="language-r">#' @param n_levels (`count`)\cr required number of factor levels in `x`.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">273</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                categorical_only = !is.null(num_levels),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">274</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                explicit_na = FALSE,</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">275</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                label_modal_title = "Please click to group the original factor levels") {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">276</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(id)</pre>
+                      <pre class="language-r">validate_n_levels &lt;- function(x, name, n_levels) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">277</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">154</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(experiment_name)</pre>
+                      <pre class="language-r">  validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">278</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">155</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(original_data)</pre>
+                      <pre class="language-r">    is.factor(x),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">279</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">156</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(transformed_data)</pre>
+                      <pre class="language-r">    paste("Variable", name, "is not a factor but a", class(x))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">280</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">157</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(assign_lists, "reactivevalues")</pre>
+                      <pre class="language-r">  ))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">281</td>
+                    <td class="num">158</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_count(num_levels, null.ok = TRUE, positive = TRUE)</pre>
+                      <pre class="language-r">  assert_string(name, min.chars = 1L)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">282</td>
+                    <td class="num">159</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_flag(categorical_only)</pre>
+                      <pre class="language-r">  assert_count(n_levels, positive = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">283</td>
+                    <td class="num">160</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_flag(explicit_na)</pre>
+                      <pre class="language-r">  validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">284</td>
+                    <td class="num">161</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_modal_title)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">285</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    identical(n_levels, nlevels(x)),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">286</td>
+                    <td class="num">162</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">    paste(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">287</td>
+                    <td class="num">163</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    to_observe &lt;- reactive({</pre>
+                      <pre class="language-r">      "Please combine the original levels of", name,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">288</td>
+                    <td class="num">164</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      list(experiment_name(), original_data())</pre>
+                      <pre class="language-r">      "into exactly", n_levels, "levels"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">289</td>
+                    <td class="num">165</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">290</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">291</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    start_col_data &lt;- eventReactive(to_observe(), {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">292</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      object &lt;- original_data()</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">293</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      col_data &lt;- SummarizedExperiment::colData(object)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">294</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      if (explicit_na) {</pre>
+                      <pre class="language-r">  ))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">295</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">167</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        hermes::df_cols_to_factor(col_data)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">296</td>
+                    <td class="num">168</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">297</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">169</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        col_data</pre>
+                      <pre class="language-r">#' Module Server for Sample Variable Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">298</td>
+                    <td class="num">170</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">299</td>
+                    <td class="num">171</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">300</td>
+                    <td class="num">172</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">301</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # The colData variables to choose the sample variable from.</pre>
+                      <pre class="language-r">#' This defines the server part for the sample variable specification.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">302</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">174</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    col_data_vars &lt;- reactive({</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">303</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">175</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col_data &lt;- start_col_data()</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">304</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">176</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      can_be_used &lt;- vapply(col_data, FUN = function(x) is.atomic(x) &amp;&amp; !allMissing(x), FUN.VALUE = logical(1))</pre>
+                      <pre class="language-r">#' @param experiment_name (reactive `string`)\cr name of the input experiment.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">305</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">177</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (categorical_only) {</pre>
+                      <pre class="language-r">#' @param original_data (reactive `SummarizedExperiment`)\cr input experiment where the</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">306</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">178</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        col_is_factor &lt;- vapply(col_data, FUN = is.factor, FUN.VALUE = logical(1))</pre>
+                      <pre class="language-r">#'   sample variables extracted via [SummarizedExperiment::colData()] should be eligible for</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">307</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">179</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        can_be_used &lt;- can_be_used &amp; col_is_factor</pre>
+                      <pre class="language-r">#'   selection.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">308</td>
+                    <td class="num">180</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' @param transformed_data (reactive `SummarizedExperiment`)\cr used when multiple sample</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">309</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">181</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      names(col_data)[can_be_used]</pre>
+                      <pre class="language-r">#'   variables can be selected in the app. In that case, pass here the pre-transformed data.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">310</td>
+                    <td class="num">182</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @param assign_lists (`reactivevalues`)\cr object to share factor level groupings across multiple</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">311</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   sample variables.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">312</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the colData variables change, update the choices for sample_var.</pre>
+                      <pre class="language-r">#' @param num_levels (`count` or `NULL`)\cr required number of levels after combining original levels.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">313</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">185</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(col_data_vars(), {</pre>
+                      <pre class="language-r">#'   If `NULL` then all numbers of levels are allowed.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">314</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">186</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      col_data_vars &lt;- col_data_vars()</pre>
+                      <pre class="language-r">#' @param categorical_only (`flag`)\cr whether only categorical variables should be selected</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">315</td>
+                    <td class="num">187</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   from.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">316</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">188</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sel &lt;- intersect(input$sample_var, col_data_vars)</pre>
+                      <pre class="language-r">#' @param explicit_na (`flag`)\cr whether the `colData` of `original_data` will be transformed with</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">317</td>
+                    <td class="num">189</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   [hermes::h_df_factors_with_explicit_na] before further processing. That means also that</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">318</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">190</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::updateOptionalSelectInput(</pre>
+                      <pre class="language-r">#'   `NA` will be made an explicit factor level and counted for `num_levels`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">319</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">191</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        session,</pre>
+                      <pre class="language-r">#' @param label_modal_title (`string`)\cr title for the dialog that asks for the text input.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">320</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">192</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "sample_var",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">321</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">193</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = col_data_vars,</pre>
+                      <pre class="language-r">#' @return Reactive [`SummarizedExperiment::SummarizedExperiment`] which can be used as</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">322</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">194</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        selected = sel</pre>
+                      <pre class="language-r">#'   input for the relevant `hermes` functions.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">323</td>
+                    <td class="num">195</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' @seealso [sampleVarSpecInput()] for the module UI.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">324</td>
+                    <td class="num">196</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">325</td>
+                    <td class="num">197</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @note Only atomic columns (e.g. not `DataFrame` columns) of the `colData`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">326</td>
+                    <td class="num">198</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Reactive for the current combination. Takes the assignment list if available</pre>
+                      <pre class="language-r">#'   which are not completely missing (`NA`) will be shown for selection.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">327</td>
+                    <td class="num">199</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # and converts to combination list.</pre>
+                      <pre class="language-r">#'   If `num_levels` is specified then only factor columns will be available.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">328</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">200</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    current_combination &lt;- reactive({</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">329</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">201</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">330</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">202</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">331</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">203</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(experiment_name)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">332</td>
+                    <td class="num">204</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' ui &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">333</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">205</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!is.null(sample_var)) {</pre>
+                      <pre class="language-r">#'                data) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">334</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">206</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assign_list &lt;- assign_lists[[experiment_name]][[sample_var]]</pre>
+                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">335</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">207</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!is.null(assign_list)) {</pre>
+                      <pre class="language-r">#'   mae &lt;- data[["MAE"]]()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">336</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">208</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          h_assign_to_group_list(assign_list)</pre>
+                      <pre class="language-r">#'   experiment_name_choices &lt;- names(mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">337</td>
+                    <td class="num">209</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">338</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">210</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          NULL</pre>
+                      <pre class="language-r">#'     encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">339</td>
+                    <td class="num">211</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#'       selectInput(ns("experiment_name"), "Select experiment", experiment_name_choices),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">340</td>
+                    <td class="num">212</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'       sampleVarSpecInput(ns("facet_var"), "Select faceting variable")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">341</td>
+                    <td class="num">213</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'     ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">342</td>
+                    <td class="num">214</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'     output = plotOutput(ns("plot"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">343</td>
+                    <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Here we produce the final object by checking</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">344</td>
+                    <td class="num">216</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # if we should combine for this sample var.</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">345</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">217</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    final_data &lt;- reactive({</pre>
+                      <pre class="language-r">#' server &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">346</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">218</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
+                      <pre class="language-r">#'                    data) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">347</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">219</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data &lt;- original_data()</pre>
+                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">348</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">220</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      start_col_data &lt;- start_col_data()</pre>
+                      <pre class="language-r">#'     experiment_data &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">349</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">221</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      transformed_data &lt;- transformed_data()</pre>
+                      <pre class="language-r">#'       req(input$experiment_name)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">350</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">222</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      current_combination &lt;- current_combination()</pre>
+                      <pre class="language-r">#'       mae &lt;- data[["MAE"]]()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">351</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'       object &lt;- mae[[input$experiment_name]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">352</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">224</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!is.null(sample_var)) {</pre>
+                      <pre class="language-r">#'       SummarizedExperiment::colData(object) &lt;-</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">353</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">225</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        sample_var_vector &lt;- start_col_data[[sample_var]]</pre>
+                      <pre class="language-r">#'         hermes::df_cols_to_factor(SummarizedExperiment::colData(object))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">354</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">226</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!is.null(current_combination)) {</pre>
+                      <pre class="language-r">#'       object</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">355</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">227</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sample_var_vector &lt;- h_collapse_levels(</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">356</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">228</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            sample_var_vector,</pre>
+                      <pre class="language-r">#'     facet_var_spec &lt;- sampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">357</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">229</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            current_combination</pre>
+                      <pre class="language-r">#'       "facet_var",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">358</td>
+                    <td class="num">230</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">#'       experiment_name = reactive({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">359</td>
+                    <td class="num">231</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#'         input$experiment_name</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">360</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">232</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!is.null(num_levels)) {</pre>
+                      <pre class="language-r">#'       }),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">361</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">233</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          validate_n_levels(sample_var_vector, sample_var, num_levels)</pre>
+                      <pre class="language-r">#'       original_data = experiment_data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">362</td>
+                    <td class="num">234</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">363</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">235</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        SummarizedExperiment::colData(transformed_data)[[sample_var]] &lt;- sample_var_vector</pre>
+                      <pre class="language-r">#'     output$plot &lt;- renderPlot({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">364</td>
+                    <td class="num">236</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'       experiment_data_final &lt;- facet_var_spec$experiment_data()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">365</td>
+                    <td class="num">237</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'       facet_var &lt;- facet_var_spec$sample_var()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">366</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">238</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      transformed_data</pre>
+                      <pre class="language-r">#'       hermes::draw_boxplot(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">367</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'         experiment_data_final,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">368</td>
+                    <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'         assay_name = "counts",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">369</td>
+                    <td class="num">241</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Function to return the UI for a modal dialog with matrix input for combination</pre>
+                      <pre class="language-r">#'         genes = hermes::gene_spec(hermes::genes(experiment_data_final)[1]),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">370</td>
+                    <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # assignment.</pre>
+                      <pre class="language-r">#'         facet_var = facet_var</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">371</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">243</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    combModal &lt;- function(sample_var_levels, # nolint</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">372</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">244</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          n_max_groups,</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">373</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">245</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          selected_groups) {</pre>
+                      <pre class="language-r">#'   })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">374</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">246</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (is.null(selected_groups)) {</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">375</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">247</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        selected_groups &lt;- pmin(</pre>
+                      <pre class="language-r">#' my_app &lt;- function() {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">376</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">248</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          seq_along(sample_var_levels),</pre>
+                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">377</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">249</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          n_max_groups</pre>
+                      <pre class="language-r">#'   mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">378</td>
+                    <td class="num">250</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">379</td>
+                    <td class="num">251</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'   app &lt;- init(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">380</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">252</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      modalDialog(</pre>
+                      <pre class="language-r">#'     data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">381</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">253</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        shinyRadioMatrix::radioMatrixInput(</pre>
+                      <pre class="language-r">#'     modules = modules(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">382</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">254</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session$ns("comb_assignment"),</pre>
+                      <pre class="language-r">#'       module(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">383</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">255</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'         label = "sampleVarSpec example",</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">256</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          rowIDs = sample_var_levels,</pre>
+                      <pre class="language-r">#'         server = server,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">384</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">257</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          rowIDsName = "Original levels",</pre>
+                      <pre class="language-r">#'         ui = ui,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">385</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">258</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          rowLLabels = rep("", length = length(sample_var_levels)),</pre>
+                      <pre class="language-r">#'         datanames = "all"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">386</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">259</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = seq_len(n_max_groups),</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">260</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = selected_groups</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">388</td>
+                    <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">389</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">262</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        span(label_modal_title),</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">390</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">263</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        footer = tagList(</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">391</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">264</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          modalButton("Cancel"),</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">392</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">265</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          actionButton(session$ns("ok"), "OK")</pre>
+                      <pre class="language-r">#'   my_app()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">266</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">394</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">267</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        include_js_files("checkbox.js")</pre>
+                      <pre class="language-r">sampleVarSpecServer &lt;- function(id, # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">395</td>
+                    <td class="num">268</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">                                experiment_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">396</td>
+                    <td class="num">269</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">                                original_data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">397</td>
+                    <td class="num">270</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                                transformed_data = original_data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">398</td>
+                    <td class="num">271</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Show modal when button is clicked and the current variable is a factor variable.</pre>
+                      <pre class="language-r">                                assign_lists = reactiveValues(),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">399</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">272</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(input$levels_button, {</pre>
+                      <pre class="language-r">                                num_levels = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">400</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">273</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
+                      <pre class="language-r">                                categorical_only = !is.null(num_levels),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">401</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">274</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data &lt;- original_data()</pre>
+                      <pre class="language-r">                                explicit_na = FALSE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">402</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">275</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      start_col_data &lt;- start_col_data()</pre>
+                      <pre class="language-r">                                label_modal_title = "Please click to group the original factor levels") {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">403</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">276</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
+                      <pre class="language-r">  assert_string(id)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">404</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">277</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_reactive(experiment_name)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">405</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">278</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(experiment_name)</pre>
+                      <pre class="language-r">  assert_reactive(original_data)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">406</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">279</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_reactive(transformed_data)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">407</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">280</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!is.null(sample_var)) {</pre>
+                      <pre class="language-r">  assert_class(assign_lists, "reactivevalues")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">408</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">281</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        current_sample_var &lt;- start_col_data[[sample_var]]</pre>
+                      <pre class="language-r">  assert_count(num_levels, null.ok = TRUE, positive = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">409</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">282</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_flag(categorical_only)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">410</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">283</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (is.factor(current_sample_var)) {</pre>
+                      <pre class="language-r">  assert_flag(explicit_na)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">411</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">284</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sample_var_levels &lt;- levels(current_sample_var)</pre>
+                      <pre class="language-r">  assert_string(label_modal_title)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">412</td>
+                    <td class="num">285</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">413</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">286</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          # Note: here we make sure we load with previous choice so the user</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">414</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">287</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          # does not constantly need to start from scratch again.</pre>
+                      <pre class="language-r">    to_observe &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">415</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">288</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          # although we do not do this if the levels do not match (i.e. if</pre>
+                      <pre class="language-r">      list(experiment_name(), original_data())</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">416</td>
+                    <td class="num">289</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          # some levels have been filtered out)</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">417</td>
+                    <td class="num">290</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">418</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">291</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected_groups &lt;- NULL</pre>
+                      <pre class="language-r">    start_col_data &lt;- eventReactive(to_observe(), {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">419</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">292</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      object &lt;- original_data()</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">293</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      col_data &lt;- SummarizedExperiment::colData(object)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">420</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">294</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          old_values &lt;- names(assign_lists[[experiment_name]][[sample_var]])</pre>
+                      <pre class="language-r">      if (explicit_na) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">421</td>
+                    <td class="num">295</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          if (!is.null(old_values) &amp;&amp;</pre>
+                      <pre class="language-r">        hermes::df_cols_to_factor(col_data)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">422</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">296</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            length(old_values) == length(sample_var_levels) &amp;&amp;</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">423</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">297</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            all(sort(old_values) == sort(sample_var_levels))) {</pre>
+                      <pre class="language-r">        col_data</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">424</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">298</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            selected_groups &lt;- assign_lists[[experiment_name]][[sample_var]]</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">425</td>
+                    <td class="num">299</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          }</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">426</td>
+                    <td class="num">300</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">427</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">301</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          showModal(combModal(</pre>
+                      <pre class="language-r">    # The colData variables to choose the sample variable from.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">428</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">302</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            sample_var_levels = sample_var_levels,</pre>
+                      <pre class="language-r">    col_data_vars &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">429</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">303</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            n_max_groups = `if`(!is.null(num_levels), num_levels, length(sample_var_levels)),</pre>
+                      <pre class="language-r">      col_data &lt;- start_col_data()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">430</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">304</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            selected_groups = selected_groups</pre>
+                      <pre class="language-r">      can_be_used &lt;- vapply(col_data, FUN = function(x) is.atomic(x) &amp;&amp; !allMissing(x), FUN.VALUE = logical(1))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">431</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">305</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ))</pre>
+                      <pre class="language-r">      if (categorical_only) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">432</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">306</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">        col_is_factor &lt;- vapply(col_data, FUN = is.factor, FUN.VALUE = logical(1))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">433</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">307</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          showNotification("Can only group levels for factor variables", type = "message")</pre>
+                      <pre class="language-r">        can_be_used &lt;- can_be_used &amp; col_is_factor</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">434</td>
+                    <td class="num">308</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">435</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">309</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">      names(col_data)[can_be_used]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">436</td>
+                    <td class="num">310</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">437</td>
+                    <td class="num">311</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">438</td>
+                    <td class="num">312</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When OK button is pressed, save the settings, and remove the modal.</pre>
+                      <pre class="language-r">    # When the colData variables change, update the choices for sample_var.</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">439</td>
+                    <td class="num">313</td>
                     <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(input$ok, {</pre>
+                      <pre class="language-r">    observeEvent(col_data_vars(), {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">440</td>
+                    <td class="num">314</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
+                      <pre class="language-r">      col_data_vars &lt;- col_data_vars()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">441</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">315</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">442</td>
+                    <td class="num">316</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      comb_assignment &lt;- input$comb_assignment</pre>
+                      <pre class="language-r">      sel &lt;- intersect(input$sample_var, col_data_vars)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">443</td>
+                    <td class="num">317</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">444</td>
+                    <td class="num">318</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(experiment_name, sample_var, comb_assignment)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">445</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      teal.widgets::updateOptionalSelectInput(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">446</td>
+                    <td class="num">319</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!is.null(num_levels) &amp;&amp; !identical(length(unique(unlist(comb_assignment))), num_levels)) {</pre>
+                      <pre class="language-r">        session,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">447</td>
+                    <td class="num">320</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(</pre>
+                      <pre class="language-r">        "sample_var",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">448</td>
+                    <td class="num">321</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste("Please group the original levels into exactly", num_levels, "levels"),</pre>
+                      <pre class="language-r">        choices = col_data_vars,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">449</td>
+                    <td class="num">322</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          type = "error"</pre>
+                      <pre class="language-r">        selected = sel</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">450</td>
+                    <td class="num">323</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">451</td>
+                    <td class="num">324</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">452</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">325</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assign_lists[[experiment_name]][[sample_var]] &lt;- comb_assignment</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">453</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">326</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        removeModal()</pre>
+                      <pre class="language-r">    # Reactive for the current combination. Takes the assignment list if available</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">454</td>
+                    <td class="num">327</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">    # and converts to combination list.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">455</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">328</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">    current_combination &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">456</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">329</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">457</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">330</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Return both the reactives with the experiment data as well as the sample variable.</pre>
+                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">458</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">331</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    list(</pre>
+                      <pre class="language-r">      req(experiment_name)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">459</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">332</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data = final_data,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">460</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">333</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      if (!is.null(sample_var)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">334</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        assign_list &lt;- assign_lists[[experiment_name]][[sample_var]]</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">335</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      sample_var = reactive({</pre>
+                      <pre class="language-r">        if (!is.null(assign_list)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">461</td>
+                    <td class="num">336</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        input$sample_var</pre>
+                      <pre class="language-r">          h_assign_to_group_list(assign_list)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">462</td>
+                    <td class="num">337</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      })</pre>
+                      <pre class="language-r">        } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">338</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">463</td>
+                    <td class="num">339</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">464</td>
+                    <td class="num">340</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">465</td>
+                    <td class="num">341</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">466</td>
+                    <td class="num">342</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">467</td>
+                    <td class="num">343</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Server for Specification of Multiple Sample Variables</pre>
+                      <pre class="language-r">    # Here we produce the final object by checking</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">468</td>
+                    <td class="num">344</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    # if we should combine for this sample var.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">469</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">345</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">    final_data &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">470</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">346</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">471</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">347</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' When multiple sample variables are used in a given module, then this</pre>
+                      <pre class="language-r">      original_data &lt;- original_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">472</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">348</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' wrapper makes it much easier to specify in the server function.</pre>
+                      <pre class="language-r">      start_col_data &lt;- start_col_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">473</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">349</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      transformed_data &lt;- transformed_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">474</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">350</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param inputIds (`character`)\cr multiple input IDs corresponding to the</pre>
+                      <pre class="language-r">      current_combination &lt;- current_combination()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">475</td>
+                    <td class="num">351</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   different sample variables specified in the UI function.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">476</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">352</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams sampleVarSpecServer</pre>
+                      <pre class="language-r">      if (!is.null(sample_var)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">477</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">353</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param ... additional arguments as documented in [sampleVarSpecServer()],</pre>
+                      <pre class="language-r">        sample_var_vector &lt;- start_col_data[[sample_var]]</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">478</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">354</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   namely the mandatory `experiment_name` and the optional `categorical_only`,</pre>
+                      <pre class="language-r">        if (!is.null(current_combination)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">479</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">355</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `num_levels` and `label_modal_title`.</pre>
+                      <pre class="language-r">          sample_var_vector &lt;- h_collapse_levels(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">480</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">356</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `transformed_data` and `assign_lists` should not be</pre>
+                      <pre class="language-r">            sample_var_vector,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">481</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">357</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   specified as they are already specified internally here.</pre>
+                      <pre class="language-r">            current_combination</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">482</td>
+                    <td class="num">358</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">483</td>
+                    <td class="num">359</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return List with the final transformed `experiment_data` reactive and a</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">484</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">360</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   list `vars` which contains the selected sample variables as reactives</pre>
+                      <pre class="language-r">        if (!is.null(num_levels)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">485</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">361</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   under their input ID.</pre>
+                      <pre class="language-r">          validate_n_levels(sample_var_vector, sample_var, num_levels)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">486</td>
+                    <td class="num">362</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">487</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">363</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">        SummarizedExperiment::colData(transformed_data)[[sample_var]] &lt;- sample_var_vector</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">488</td>
+                    <td class="num">364</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">489</td>
+                    <td class="num">365</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' \dontrun{</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">490</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">366</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # In the server use:</pre>
+                      <pre class="language-r">      transformed_data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">491</td>
+                    <td class="num">367</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' sample_var_specs &lt;- multiSampleVarSpecServer(</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">492</td>
+                    <td class="num">368</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   inputIds = c("facet_var", "color_var"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">493</td>
+                    <td class="num">369</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   experiment_name = reactive({</pre>
+                      <pre class="language-r">    # Function to return the UI for a modal dialog with matrix input for combination</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">494</td>
+                    <td class="num">370</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     input$experiment_name</pre>
+                      <pre class="language-r">    # assignment.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">495</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">371</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   }),</pre>
+                      <pre class="language-r">    combModal &lt;- function(sample_var_levels, # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">496</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">372</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   original_data = ori_data # nolint Please update the &lt;ori_data&gt;</pre>
+                      <pre class="language-r">                          n_max_groups,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">497</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">373</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">                          selected_groups) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">498</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">374</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      if (is.null(selected_groups)) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">375</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        selected_groups &lt;- pmin(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">376</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Then can extract the transformed data and selected variables later:</pre>
+                      <pre class="language-r">          seq_along(sample_var_levels),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">499</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">377</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' experiment_data &lt;- sample_var_specs$experiment_data()</pre>
+                      <pre class="language-r">          n_max_groups</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">500</td>
+                    <td class="num">378</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' facet_var &lt;- sample_var_specs$vars$facet_var()</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">501</td>
+                    <td class="num">379</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' color_var &lt;- sample_var_specs$vars$color_var()</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">502</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">380</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">      modalDialog(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">503</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">381</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">multiSampleVarSpecServer &lt;- function(inputIds, # nolint</pre>
+                      <pre class="language-r">        shinyRadioMatrix::radioMatrixInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">504</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">382</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                     original_data,</pre>
+                      <pre class="language-r">          session$ns("comb_assignment"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">505</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">383</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                     ...) {</pre>
+                      <pre class="language-r">          rowIDs = sample_var_levels,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">506</td>
+                    <td class="num">384</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(inputIds, any.missing = FALSE, unique = TRUE)</pre>
+                      <pre class="language-r">          rowIDsName = "Original levels",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">507</td>
+                    <td class="num">385</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assign_lists &lt;- reactiveValues()</pre>
+                      <pre class="language-r">          rowLLabels = rep("", length = length(sample_var_levels)),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">508</td>
+                    <td class="num">386</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  spec_list &lt;- list()</pre>
+                      <pre class="language-r">          choices = seq_len(n_max_groups),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">509</td>
+                    <td class="num">387</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  transformed_data &lt;- original_data</pre>
+                      <pre class="language-r">          selected = selected_groups</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">510</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">388</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  for (id in inputIds) {</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">511</td>
+                    <td class="num">389</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    spec_list[[id]] &lt;- sampleVarSpecServer(</pre>
+                      <pre class="language-r">        span(label_modal_title),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">512</td>
+                    <td class="num">390</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id,</pre>
+                      <pre class="language-r">        footer = tagList(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">513</td>
+                    <td class="num">391</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = original_data,</pre>
+                      <pre class="language-r">          modalButton("Cancel"),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">514</td>
+                    <td class="num">392</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      transformed_data = transformed_data,</pre>
+                      <pre class="language-r">          actionButton(session$ns("ok"), "OK")</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">393</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">515</td>
+                    <td class="num">394</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assign_lists = assign_lists,</pre>
+                      <pre class="language-r">        include_js_files("checkbox.js")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">516</td>
+                    <td class="num">395</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ...</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">517</td>
+                    <td class="num">396</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">518</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">397</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    transformed_data &lt;- spec_list[[id]]$experiment_data</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">519</td>
+                    <td class="num">398</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    # Show modal when button is clicked and the current variable is a factor variable.</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">399</td>
+                    <td class="coverage">2<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    observeEvent(input$levels_button, {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">520</td>
+                    <td class="num">400</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  list(</pre>
+                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">521</td>
+                    <td class="num">401</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment_data = transformed_data,</pre>
+                      <pre class="language-r">      original_data &lt;- original_data()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">522</td>
+                    <td class="num">402</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    vars = lapply(spec_list, "[[", "sample_var")</pre>
+                      <pre class="language-r">      start_col_data &lt;- start_col_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">523</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">403</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">524</td>
+                    <td class="num">404</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/geneSpec.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">405</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Input for Gene Signature Specification</pre>
+                      <pre class="language-r">      req(experiment_name)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">406</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">407</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">      if (!is.null(sample_var)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">4</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">408</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        current_sample_var &lt;- start_col_data[[sample_var]]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">409</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the input for the gene signature specification.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">410</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        if (is.factor(current_sample_var)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">411</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">          sample_var_levels &lt;- levels(current_sample_var)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">412</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param funs (named `list`)\cr names of this list will be used for the function</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">413</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   selection drop down menu.</pre>
+                      <pre class="language-r">          # Note: here we make sure we load with previous choice so the user</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">414</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_genes (`string`)\cr label for the gene selection.</pre>
+                      <pre class="language-r">          # does not constantly need to start from scratch again.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">415</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_funs (`string`)\cr label for the function selection.</pre>
+                      <pre class="language-r">          # although we do not do this if the levels do not match (i.e. if</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">12</td>
+                    <td class="num">416</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_text_button (`string`)\cr label for the text input button.</pre>
+                      <pre class="language-r">          # some levels have been filtered out)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">417</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_lock_button (`string`)\cr label for the lock button.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">418</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_select_all_button (`string`)\cr label for the selecting all genes button.</pre>
+                      <pre class="language-r">          selected_groups &lt;- NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">15</td>
+                    <td class="num">419</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_select_none_button (`string`)\cr label for the selecting no genes button.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">420</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param max_options (`count`)\cr maximum number of gene options rendering and selected via</pre>
+                      <pre class="language-r">          old_values &lt;- names(assign_lists[[experiment_name]][[sample_var]])</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">421</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          if (!is.null(old_values) &amp;&amp;</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">17</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">422</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   "Select All".</pre>
+                      <pre class="language-r">            length(old_values) == length(sample_var_levels) &amp;&amp;</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">423</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param max_selected (`count`)\cr maximum number of genes which can be selected.</pre>
+                      <pre class="language-r">            all(sort(old_values) == sort(sample_var_levels))) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">424</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            selected_groups &lt;- assign_lists[[experiment_name]][[sample_var]]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">425</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The UI part.</pre>
+                      <pre class="language-r">          }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">426</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [geneSpecServer()] for the module server and a complete example.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">427</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">          showModal(combModal(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">428</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            sample_var_levels = sample_var_levels,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">429</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">            n_max_groups = `if`(!is.null(num_levels), num_levels, length(sample_var_levels)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">430</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' geneSpecInput("my_genes", list(mean = colMeans), label_funs = "Please select function")</pre>
+                      <pre class="language-r">            selected_groups = selected_groups</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">431</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">geneSpecInput &lt;- function(inputId, # nolint</pre>
+                      <pre class="language-r">          ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">432</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          funs,</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">433</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          label_genes = "Select Gene(s)",</pre>
+                      <pre class="language-r">          showNotification("Can only group levels for factor variables", type = "message")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">434</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          label_funs = "Select Gene Summary",</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">435</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          label_text_button = "Enter list of genes",</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">436</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          label_lock_button = "Lock gene selection (so that it does not get updated when filtering)",</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">437</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          label_select_all_button = paste0("Select All Genes (first ", max_options, ")"),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">438</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          label_select_none_button = "Select None",</pre>
+                      <pre class="language-r">    # When OK button is pressed, save the settings, and remove the modal.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">439</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          max_options = 200L,</pre>
+                      <pre class="language-r">    observeEvent(input$ok, {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">440</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          max_selected = max_options) {</pre>
+                      <pre class="language-r">      experiment_name &lt;- experiment_name()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">36</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">441</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(inputId)</pre>
+                      <pre class="language-r">      sample_var &lt;- input$sample_var</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">37</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">442</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_list(funs, names = "unique", min.len = 1L)</pre>
+                      <pre class="language-r">      comb_assignment &lt;- input$comb_assignment</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">38</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">443</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_genes)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">39</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">444</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_funs)</pre>
+                      <pre class="language-r">      req(experiment_name, sample_var, comb_assignment)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">40</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">445</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_text_button)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">41</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">446</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_lock_button)</pre>
+                      <pre class="language-r">      if (!is.null(num_levels) &amp;&amp; !identical(length(unique(unlist(comb_assignment))), num_levels)) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">42</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">447</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_select_all_button)</pre>
+                      <pre class="language-r">        showNotification(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">43</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">448</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_select_none_button)</pre>
+                      <pre class="language-r">          paste("Please group the original levels into exactly", num_levels, "levels"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">44</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">449</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_count(max_options, positive = TRUE)</pre>
+                      <pre class="language-r">          type = "error"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">45</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">450</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_count(max_selected, positive = TRUE)</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">451</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">47</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">452</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
+                      <pre class="language-r">        assign_lists[[experiment_name]][[sample_var]] &lt;- comb_assignment</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">48</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">453</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  tagList(</pre>
+                      <pre class="language-r">        removeModal()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">49</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">454</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    include_css_files(pattern = "*"),</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">50</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">455</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    div(</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">51</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">456</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      class = "row",</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">457</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    # Return both the reactives with the experiment data as well as the sample variable.</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">52</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="num">458</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      div(</pre>
+                      <pre class="language-r">    list(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">53</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="num">459</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        class = "col-sm-8",</pre>
+                      <pre class="language-r">      experiment_data = final_data,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">54</td>
-                    <td class="coverage">7<em>x</em></td>
+                    <td class="num">460</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        tags$label(</pre>
+                      <pre class="language-r">      sample_var = reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">461</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "control-label",</pre>
+                      <pre class="language-r">        input$sample_var</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">56</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">462</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          label_genes</pre>
+                      <pre class="language-r">      })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">463</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">464</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">59</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">465</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      div(</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">60</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">466</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        class = "col-sm-2",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">61</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">467</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        actionButton(</pre>
+                      <pre class="language-r">#' Module Server for Specification of Multiple Sample Variables</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">62</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">468</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns("select_none_button"),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">63</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">469</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          span(icon("remove-circle", lib = "glyphicon")),</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">64</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">470</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = label_select_none_button,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">65</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">471</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "pull-right list-genes"</pre>
+                      <pre class="language-r">#' When multiple sample variables are used in a given module, then this</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">472</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">#' wrapper makes it much easier to specify in the server function.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">67</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">473</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        actionButton(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">68</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">474</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns("select_all_button"),</pre>
+                      <pre class="language-r">#' @param inputIds (`character`)\cr multiple input IDs corresponding to the</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">69</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">475</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          span(icon("ok-circle", lib = "glyphicon")),</pre>
+                      <pre class="language-r">#'   different sample variables specified in the UI function.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">70</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">476</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = label_select_all_button,</pre>
+                      <pre class="language-r">#' @inheritParams sampleVarSpecServer</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">71</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">477</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "pull-right list-genes"</pre>
+                      <pre class="language-r">#' @param ... additional arguments as documented in [sampleVarSpecServer()],</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">478</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'   namely the mandatory `experiment_name` and the optional `categorical_only`,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">479</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">#'   `num_levels` and `label_modal_title`.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">74</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">480</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      div(</pre>
+                      <pre class="language-r">#'   `transformed_data` and `assign_lists` should not be</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">75</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">481</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        class = "col-sm-2",</pre>
+                      <pre class="language-r">#'   specified as they are already specified internally here.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">76</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">482</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        actionButton(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">77</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">483</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns("text_button"),</pre>
+                      <pre class="language-r">#' @return List with the final transformed `experiment_data` reactive and a</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">484</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          span(icon("fas fa-font")),</pre>
+                      <pre class="language-r">#'   list `vars` which contains the selected sample variables as reactives</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">79</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">485</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = label_text_button,</pre>
+                      <pre class="language-r">#'   under their input ID.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">80</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">486</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "pull-right list-genes"</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">487</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">82</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">488</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        div(</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">83</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">489</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          class = "pull-right",</pre>
+                      <pre class="language-r">#' \dontrun{</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">84</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">490</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = label_lock_button,</pre>
+                      <pre class="language-r">#' # In the server use:</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">491</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          shinyWidgets::prettyToggle(</pre>
+                      <pre class="language-r">#' sample_var_specs &lt;- multiSampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">492</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            ns("lock_button"),</pre>
+                      <pre class="language-r">#'   inputIds = c("facet_var", "color_var"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">87</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">493</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            value = FALSE,</pre>
+                      <pre class="language-r">#'   experiment_name = reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">88</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">494</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            label_on = NULL,</pre>
+                      <pre class="language-r">#'     input$experiment_name</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">495</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            label_off = NULL,</pre>
+                      <pre class="language-r">#'   }),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">496</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            status_on = "default",</pre>
+                      <pre class="language-r">#'   original_data = ori_data # nolint Please update the &lt;ori_data&gt;</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">91</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">497</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            status_off = "default",</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">92</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">498</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            outline = FALSE,</pre>
+                      <pre class="language-r">#' # Then can extract the transformed data and selected variables later:</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">93</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">499</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            plain = TRUE,</pre>
+                      <pre class="language-r">#' experiment_data &lt;- sample_var_specs$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">500</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            icon_on = icon("fas fa-lock"),</pre>
+                      <pre class="language-r">#' facet_var &lt;- sample_var_specs$vars$facet_var()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">501</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            icon_off = icon("fas fa-lock-open"),</pre>
+                      <pre class="language-r">#' color_var &lt;- sample_var_specs$vars$color_var()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">96</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">502</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            animation = "pulse"</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">97</td>
+                    <td class="num">503</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          )</pre>
+                      <pre class="language-r">multiSampleVarSpecServer &lt;- function(inputIds, # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">504</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">                                     original_data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">505</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">                                     ...) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">100</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">506</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">  assert_character(inputIds, any.missing = FALSE, unique = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">101</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">507</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    div(</pre>
+                      <pre class="language-r">  assign_lists &lt;- reactiveValues()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">102</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">508</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      class = "custom-select-input",</pre>
+                      <pre class="language-r">  spec_list &lt;- list()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">103</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">509</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      selectizeInput(</pre>
+                      <pre class="language-r">  transformed_data &lt;- original_data</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">104</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">510</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns("genes"),</pre>
+                      <pre class="language-r">  for (id in inputIds) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">105</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">511</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = NULL,</pre>
+                      <pre class="language-r">    spec_list[[id]] &lt;- sampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">106</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">512</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = "",</pre>
+                      <pre class="language-r">      id,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">107</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">513</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        multiple = TRUE,</pre>
+                      <pre class="language-r">      original_data = original_data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">108</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">514</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        selected = 1,</pre>
+                      <pre class="language-r">      transformed_data = transformed_data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">109</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">515</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        options = list(</pre>
+                      <pre class="language-r">      assign_lists = assign_lists,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">110</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">516</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          placeholder = "- Nothing selected -",</pre>
+                      <pre class="language-r">      ...</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">111</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">517</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          render = I("{</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">112</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">518</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          option: function(item, escape) {</pre>
+                      <pre class="language-r">    transformed_data &lt;- spec_list[[id]]$experiment_data</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">113</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">519</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">              return '&lt;div&gt; &lt;span style=\"font-size: inherit;\"&gt;' + item.label + '&lt;/div&gt;' +</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">114</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">520</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                ' &lt;span style=\"color: #808080; font-size: xx-small;\" &gt;' + item.value + '&lt;/div&gt; &lt;/div&gt;'</pre>
+                      <pre class="language-r">  list(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">521</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    experiment_data = transformed_data,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">522</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    vars = lapply(spec_list, "[[", "sample_var")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">115</td>
+                    <td class="num">523</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">            }</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">524</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          }"),</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">117</td>
-                    <td class="coverage">7<em>x</em></td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/scatterplot.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          searchField = c("value", "label"),</pre>
+                      <pre class="language-r">#' Teal Module for RNA-seq Scatterplot</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">118</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          maxOptions = max_options,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">119</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          maxItems = max_selected</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">120</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#' This module provides an interactive scatterplot for RNA-seq gene expression</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' analysis.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">123</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    conditionalPanel(</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">124</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      condition = "input.genes &amp;&amp; input.genes.length &gt; 1",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">125</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ns = ns,</pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">126</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      selectInput(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">127</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns("fun_name"),</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">128</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">13</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label_funs,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">7<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">14</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        names(funs)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">130</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">131</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">132</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">134</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">135</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function to Update Gene Selection</pre>
+                      <pre class="language-r">#'   modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">136</td>
+                    <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     tm_g_scatterplot(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#'       label = "scatterplot",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">138</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">139</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This helper function takes the intersection of `selected` and</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">140</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' `choices` for genes and updates the `inputId` accordingly. It then</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' shows a notification if not all `selected` genes were available.</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param session (`ShinySession`)\cr the session object.</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param selected (`character`)\cr currently selected gene IDs.</pre>
+                      <pre class="language-r">tm_g_scatterplot &lt;- function(label,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">146</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param choices (`data.frame`)\cr containing `id` and `name` columns of the</pre>
+                      <pre class="language-r">                             mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">147</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   new choices.</pre>
+                      <pre class="language-r">                             exclude_assays = "counts",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">148</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                             summary_funs = list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">149</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">                               Mean = colMeans,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">150</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_update_gene_selection &lt;- function(session,</pre>
+                      <pre class="language-r">                               Median = matrixStats::colMedians,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">151</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                    inputId, # nolint</pre>
+                      <pre class="language-r">                               Max = matrixStats::colMaxs</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">152</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                    selected,</pre>
+                      <pre class="language-r">                             ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">153</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                    choices) {</pre>
+                      <pre class="language-r">                             pre_output = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">154</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">39</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  is_new_selected &lt;- selected %in% choices$id</pre>
+                      <pre class="language-r">                             post_output = NULL) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">155</td>
+                    <td class="num">40</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  is_removed &lt;- !is_new_selected</pre>
+                      <pre class="language-r">  logger::log_info("Initializing tm_g_scatterplot")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">156</td>
+                    <td class="num">41</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  updateSelectizeInput(</pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">157</td>
+                    <td class="num">42</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    session = session,</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">158</td>
+                    <td class="num">43</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    inputId = inputId,</pre>
+                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">159</td>
+                    <td class="num">44</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    selected = selected[is_new_selected],</pre>
+                      <pre class="language-r">  assert_summary_funs(summary_funs)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">160</td>
+                    <td class="num">45</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    choices = stats::setNames(choices$id, choices$name),</pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">161</td>
+                    <td class="num">46</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = TRUE</pre>
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">163</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">48</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">164</td>
+                    <td class="num">49</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  n_removed &lt;- sum(is_removed)</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">165</td>
+                    <td class="num">50</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (n_removed &gt; 0) {</pre>
+                      <pre class="language-r">    server = srv_g_scatterplot,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">166</td>
+                    <td class="num">51</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    showNotification(paste(</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">167</td>
+                    <td class="num">52</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "Removed", n_removed, ifelse(n_removed &gt; 1, "genes", "gene"),</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">168</td>
+                    <td class="num">53</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::h_parens(hermes::h_short_list(selected[is_removed]))</pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">169</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">54</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ))</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">170</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">171</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">56</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    ui = ui_g_scatterplot,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">172</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">57</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">173</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">58</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function to Parse Genes</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">174</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">59</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">175</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">60</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">176</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">61</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">177</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This helper function takes a vector of `words` and tries to match them</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">178</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">63</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' with the `id` and `name` columns of possible gene choices.</pre>
+                      <pre class="language-r">    datanames = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">179</td>
+                    <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">180</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param words (`character`)\cr containing gene IDs or names.</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">181</td>
+                    <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams h_update_gene_selection</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">182</td>
+                    <td class="num">67</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The subset of `choices` which matches `words` in ID or name.</pre>
+                      <pre class="language-r">#' @describeIn tm_g_scatterplot sets up the user interface.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">183</td>
+                    <td class="num">68</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">184</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">185</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">ui_g_scatterplot &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">186</td>
+                    <td class="num">71</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' h_parse_genes(</pre>
+                      <pre class="language-r">                             data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">187</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   c("a", "2535"),</pre>
+                      <pre class="language-r">                             mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">188</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data.frame(id = as.character(2533:2537), name = letters[1:5])</pre>
+                      <pre class="language-r">                             summary_funs,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">189</td>
+                    <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">                             pre_output,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">190</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_parse_genes &lt;- function(words, choices) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">191</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(words, min.len = 1L)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">192</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_data_frame(choices, types = "character")</pre>
+                      <pre class="language-r">                             post_output) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">193</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">76</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_set_equal(names(choices), c("id", "name"))</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">194</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">195</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">78</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  id_matches &lt;- choices$id %in% words</pre>
+                      <pre class="language-r">  smooth_method_choices &lt;- c(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">196</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">79</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  name_matches &lt;- choices$name %in% words</pre>
+                      <pre class="language-r">    Linear = "lm",</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">197</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">80</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  has_match &lt;- id_matches | name_matches</pre>
+                      <pre class="language-r">    Loess = "loess",</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">198</td>
-                    <td class="coverage">2<em>x</em></td>
+                    <td class="num">81</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  choices[has_match, , drop = FALSE]</pre>
+                      <pre class="language-r">    None = "none"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">199</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">200</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">201</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' Module Server for Gene Signature Specification</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">202</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">203</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">84</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">204</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">205</td>
+                    <td class="num">86</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the server part for the gene signature specification.</pre>
+                      <pre class="language-r">      ### Reporter</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">206</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">87</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">207</td>
+                    <td class="num">88</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      ###</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">208</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">89</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param funs (static named `list`)\cr names of this list will be used for the function</pre>
+                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">209</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">90</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   selection drop down menu.</pre>
+                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">210</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">91</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param gene_choices (reactive `data.frame`)\cr returns the possible gene choices to</pre>
+                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">211</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">92</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   populate in the UI, as a `data.frame` with columns `id` and `name`.</pre>
+                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">212</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">93</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_modal_title (`string`)\cr title for the dialog that asks for the text input.</pre>
+                      <pre class="language-r">      geneSpecInput(ns("x_spec"), summary_funs, label_genes = "Select x Gene(s)"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">213</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">94</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_modal_footer (`character`)\cr lines of text to use for the footer of the dialog.</pre>
+                      <pre class="language-r">      geneSpecInput(ns("y_spec"), summary_funs, label_genes = "Select y Gene(s)"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">214</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">95</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      teal.widgets::panel_group(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">215</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">96</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Reactive [`hermes::GeneSpec`] which can be used as input for the relevant</pre>
+                      <pre class="language-r">        teal.widgets::panel_item(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">216</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">97</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `hermes` functions.</pre>
+                      <pre class="language-r">          input_id = "settings_item",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">217</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">98</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [geneSpecInput()] for the module UI.</pre>
+                      <pre class="language-r">          collapsed = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">218</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">99</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          title = "Additional Settings",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">219</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">100</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("color_var"), "Optional color variable"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">220</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">101</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("facet_var"), "Optional facet variable"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">221</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">102</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">          selectInput(ns("smooth_method"), "Select smoother", smooth_method_choices)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">222</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ui &lt;- function(id,</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                data,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">224</td>
+                    <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                funs) {</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">225</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
+                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">226</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">107</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">    pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">227</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">108</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     encoding = div(</pre>
+                      <pre class="language-r">    post_output = post_output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">228</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       geneSpecInput(</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">229</td>
+                    <td class="num">110</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ns("my_genes"),</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">230</td>
+                    <td class="num">111</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         funs = funs,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">231</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label_funs = "Please select function"</pre>
+                      <pre class="language-r">#' @describeIn tm_g_scatterplot sets up the server with reactive graph.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">232</td>
+                    <td class="num">113</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">233</td>
+                    <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     ),</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">234</td>
+                    <td class="num">115</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output = textOutput(ns("result"))</pre>
+                      <pre class="language-r">srv_g_scatterplot &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">235</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">                              data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">236</td>
+                    <td class="num">117</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">                              filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">237</td>
+                    <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' server &lt;- function(id,</pre>
+                      <pre class="language-r">                              reporter,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">238</td>
+                    <td class="num">119</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                    data,</pre>
+                      <pre class="language-r">                              mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">239</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                    funs) {</pre>
+                      <pre class="language-r">                              exclude_assays,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">240</td>
+                    <td class="num">121</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">                              summary_funs) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">241</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">122</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     gene_choices &lt;- reactive({</pre>
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">242</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">123</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae &lt;- data[["MAE"]]()</pre>
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">243</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">124</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       object &lt;- mae[[1]]</pre>
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">244</td>
+                    <td class="num">125</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_ids &lt;- rownames(object)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">245</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">126</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_names &lt;- SummarizedExperiment::rowData(object)$symbol</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">246</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">127</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_data &lt;- data.frame(</pre>
+                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">247</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">128</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         id = gene_ids,</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">248</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">129</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         name = gene_names</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">249</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">130</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">250</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">131</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_data[order(gene_data$name), ]</pre>
+                      <pre class="language-r">      mae_name = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">251</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">252</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">133</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     gene_spec &lt;- geneSpecServer(</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">253</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">134</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "my_genes",</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">254</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">135</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       funs = funs,</pre>
+                      <pre class="language-r">      assays = experiment$assays,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">255</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">136</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_choices = gene_choices</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">256</td>
+                    <td class="num">137</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">257</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">138</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output$result &lt;- renderText({</pre>
+                      <pre class="language-r">    sample_var_specs &lt;- multiSampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">258</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">139</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       validate_gene_spec(</pre>
+                      <pre class="language-r">      inputIds = c("facet_var", "color_var"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">259</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">140</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         gene_spec(),</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">260</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">141</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         gene_choices()$id</pre>
+                      <pre class="language-r">      original_data = experiment$data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">262</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">143</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_spec &lt;- gene_spec()</pre>
+                      <pre class="language-r">    x_spec &lt;- geneSpecServer("x_spec", summary_funs, experiment$genes)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">263</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">144</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       gene_spec$get_label()</pre>
+                      <pre class="language-r">    y_spec &lt;- geneSpecServer("y_spec", summary_funs, experiment$genes)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">264</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">265</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">146</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   })</pre>
+                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">266</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">      # Resolve all reactivity.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">267</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">148</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' funs &lt;- list(mean = colMeans)</pre>
+                      <pre class="language-r">      experiment_data &lt;- sample_var_specs$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">268</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">149</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' my_app &lt;- function() {</pre>
+                      <pre class="language-r">      x_spec &lt;- x_spec()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">269</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">150</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">      y_spec &lt;- y_spec()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">270</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">151</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">      facet_var &lt;- sample_var_specs$vars$facet_var()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">271</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">152</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">      color_var &lt;- sample_var_specs$vars$color_var()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">272</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">153</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   app &lt;- init(</pre>
+                      <pre class="language-r">      assay_name &lt;- assay()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">273</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">154</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     data = data,</pre>
+                      <pre class="language-r">      smooth_method &lt;- input$smooth_method</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">274</td>
+                    <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     modules = modules(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">275</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">156</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       module(</pre>
+                      <pre class="language-r">      validate_gene_spec(x_spec, rownames(experiment_data))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">276</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">157</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label = "GeneSpec example",</pre>
+                      <pre class="language-r">      validate_gene_spec(y_spec, rownames(experiment_data))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">277</td>
+                    <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server = server,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">278</td>
+                    <td class="num">159</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server_args = list(funs = funs),</pre>
+                      <pre class="language-r">      # Require which states need to be truthy.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">279</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">160</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui = ui,</pre>
+                      <pre class="language-r">      req(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">280</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">161</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui_args = list(funs = funs),</pre>
+                      <pre class="language-r">        smooth_method,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">281</td>
+                    <td class="num">162</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         datanames = "all"</pre>
+                      <pre class="language-r">        # Note: The following statements are important to make sure the UI inputs have been updated.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">282</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">163</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">        isTRUE(assay_name %in% SummarizedExperiment::assayNames(experiment_data)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">283</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">164</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">        is.null(facet_var) || isTRUE(facet_var %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">284</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">165</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">        is.null(color_var) || isTRUE(color_var %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">285</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">166</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">        cancelOutput = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">286</td>
+                    <td class="num">167</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">287</td>
+                    <td class="num">168</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">288</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">169</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   my_app()</pre>
+                      <pre class="language-r">      hermes::draw_scatterplot(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">289</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">170</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        object = experiment_data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">290</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">171</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">geneSpecServer &lt;- function(id, # nolint</pre>
+                      <pre class="language-r">        assay_name = assay_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">291</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">172</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           funs,</pre>
+                      <pre class="language-r">        x_spec = x_spec,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">292</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">173</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           gene_choices,</pre>
+                      <pre class="language-r">        y_spec = y_spec,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">293</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">174</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           label_modal_title = "Enter list of genes",</pre>
+                      <pre class="language-r">        facet_var = facet_var,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">294</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">175</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           label_modal_footer = c(</pre>
+                      <pre class="language-r">        color_var = color_var,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">295</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">176</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             "Please enter a comma-separated list of gene IDs and/or names.",</pre>
+                      <pre class="language-r">        smooth_method = smooth_method</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">296</td>
+                    <td class="num">177</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                             "(Note that genes not included in current choices will be removed)"</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">297</td>
+                    <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           )) {</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">298</td>
+                    <td class="num">179</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(id)</pre>
+                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">299</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">180</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_list(funs, names = "unique", min.len = 1L)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">300</td>
+                    <td class="num">181</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(gene_choices)</pre>
+                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">301</td>
+                    <td class="num">182</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_modal_title)</pre>
+                      <pre class="language-r">      id = "plot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">302</td>
+                    <td class="num">183</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(label_modal_footer)</pre>
+                      <pre class="language-r">      plot_r = plot_r</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">303</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">304</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">185</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">305</td>
+                    <td class="num">186</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # The `reactiveValues` object for storing current gene text input.</pre>
+                      <pre class="language-r">    ### REPORTER</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">306</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">187</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # This will also be a data frame with id and name columns.</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">307</td>
+                    <td class="num">188</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    parsed_genes &lt;- reactiveVal(NULL, label = "Parsed genes")</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">308</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">189</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">309</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">190</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # If the parsed genes are entered via text, update gene selection.</pre>
+                      <pre class="language-r">          title = "Scatter Plot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">310</td>
+                    <td class="num">191</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(parsed_genes(), ignoreNULL = TRUE, {</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">311</td>
+                    <td class="num">192</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">312</td>
+                    <td class="num">193</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      parsed_genes &lt;- parsed_genes()</pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">313</td>
+                    <td class="num">194</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">314</td>
+                    <td class="num">195</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      h_update_gene_selection(</pre>
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">315</td>
+                    <td class="num">196</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        session,</pre>
+                      <pre class="language-r">        encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">316</td>
+                    <td class="num">197</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        inputId = "genes",</pre>
+                      <pre class="language-r">          "Experiment:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">317</td>
+                    <td class="num">198</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        selected = parsed_genes$id,</pre>
+                      <pre class="language-r">          input$`experiment-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">318</td>
+                    <td class="num">199</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = gene_choices</pre>
+                      <pre class="language-r">          "\nAssay:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">319</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">200</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">          input$`assay-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">320</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">201</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          "\nX Genes Selected:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">321</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">202</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          paste0(x_spec()$get_gene_labels(), collapse = ", "),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">322</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">203</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When</pre>
+                      <pre class="language-r">          "\nX Genes Summary:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">323</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">204</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # 1) the gene choices are recomputed,</pre>
+                      <pre class="language-r">          input$`x_spec-fun_name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">324</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">205</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # 2) the lock is pressed and then switched off,</pre>
+                      <pre class="language-r">          "\nY Genes Selected:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">325</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">206</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # then update gene selection.</pre>
+                      <pre class="language-r">          paste0(y_spec()$get_gene_labels(), collapse = ", "),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">326</td>
+                    <td class="num">207</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(list(gene_choices(), input$lock_button), {</pre>
+                      <pre class="language-r">          "\nY Genes Summary:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">327</td>
+                    <td class="num">208</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">          input$`y_spec-fun_name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">328</td>
+                    <td class="num">209</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lock_button &lt;- input$lock_button</pre>
+                      <pre class="language-r">          "\nOptional Color Variable:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">329</td>
+                    <td class="num">210</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      old_selected &lt;- input$genes</pre>
+                      <pre class="language-r">          input$`color_var-sample_var`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">330</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">211</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          "\nOptional Facetting Variable:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">331</td>
+                    <td class="num">212</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (isFALSE(lock_button)) {</pre>
+                      <pre class="language-r">          input$`facet_var-sample_var`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">332</td>
+                    <td class="num">213</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        h_update_gene_selection(</pre>
+                      <pre class="language-r">          "\nSmoother:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">333</td>
+                    <td class="num">214</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session,</pre>
+                      <pre class="language-r">          input$smooth_method</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">215</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">334</td>
+                    <td class="num">216</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          inputId = "genes",</pre>
+                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">335</td>
+                    <td class="num">217</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = old_selected,</pre>
+                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">336</td>
+                    <td class="num">218</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = gene_choices</pre>
+                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">337</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">219</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">338</td>
+                    <td class="num">220</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">339</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">221</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">340</td>
+                    <td class="num">222</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">341</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the Select All button is pressed and not locked, select all genes.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">342</td>
+                    <td class="num">224</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(input$select_all_button, {</pre>
+                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">343</td>
+                    <td class="num">225</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">344</td>
+                    <td class="num">226</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lock_button &lt;- input$lock_button</pre>
+                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">345</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">227</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">346</td>
+                    <td class="num">228</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (isFALSE(lock_button)) {</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">347</td>
+                    <td class="num">229</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        h_update_gene_selection(</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">348</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">230</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session,</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">349</td>
+                    <td class="num">231</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          inputId = "genes",</pre>
+                      <pre class="language-r">        card</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">350</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">232</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = gene_choices$id,</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">351</td>
+                    <td class="num">233</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = gene_choices</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">352</td>
+                    <td class="num">234</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">353</td>
+                    <td class="num">235</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">354</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">236</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">355</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">237</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Please unlock if you would like to select all genes",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">356</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">238</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          type = "warning"</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">357</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#' @describeIn tm_g_scatterplot sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">358</td>
+                    <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">359</td>
+                    <td class="num">241</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">360</td>
+                    <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">361</td>
+                    <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the Select None button is pressed and not locked, select none.</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">362</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">244</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(input$select_none_button, {</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">245</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'   sample_tm_g_scatterplot()</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">246</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' }</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">247</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">sample_tm_g_scatterplot &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">363</td>
+                    <td class="num">248</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">364</td>
+                    <td class="num">249</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      lock_button &lt;- input$lock_button</pre>
+                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">365</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">250</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">366</td>
+                    <td class="num">251</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (isFALSE(lock_button)) {</pre>
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">367</td>
+                    <td class="num">252</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        h_update_gene_selection(</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">368</td>
+                    <td class="num">253</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session,</pre>
+                      <pre class="language-r">    modules = teal::modules(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">369</td>
+                    <td class="num">254</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          inputId = "genes",</pre>
+                      <pre class="language-r">      tm_g_scatterplot(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">370</td>
+                    <td class="num">255</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = character(),</pre>
+                      <pre class="language-r">        label = "scatterplot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">371</td>
+                    <td class="num">256</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = gene_choices</pre>
+                      <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">372</td>
+                    <td class="num">257</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">373</td>
+                    <td class="num">258</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">374</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">259</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">375</td>
+                    <td class="num">260</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Please unlock if you would like to select none",</pre>
+                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">376</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">261</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          type = "warning"</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/pca.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">377</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#' Teal Module for PCA Analysis</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">378</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#'</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">5</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' This module provides an interactive principal components plot and an</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' interactive heatmap with correlation of principal components with sample</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">#' variables.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">379</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">380</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">381</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Return the UI for a modal dialog with gene text input, showing examples.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">382</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    dataModal &lt;- function(example_list) { # nolint</pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">383</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      modalDialog(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">384</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">13</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        textInput(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">385</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">14</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          session$ns("gene_text"),</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">386</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          label = label_modal_title,</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          placeholder = example_list</pre>
+                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">388</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">389</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">18</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        do.call("span", as.list(label_modal_footer)),</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">390</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        footer = tagList(</pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">391</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">20</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          modalButton("Cancel"),</pre>
+                      <pre class="language-r">#'   modules = modules(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">392</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          actionButton(session$ns("ok_button"), "OK")</pre>
+                      <pre class="language-r">#'     tm_g_pca(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'       label = "PCA plot",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">394</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">395</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">396</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">397</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Show modal when the text button is clicked.</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">398</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(input$text_button, {</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">399</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">400</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      example_list &lt;- hermes::h_short_list(utils::head(setdiff(gene_choices$name, "")))</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">401</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      showModal(dataModal(example_list))</pre>
+                      <pre class="language-r">tm_g_pca &lt;- function(label,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">402</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">                     mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">403</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                     exclude_assays = character(),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">404</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When OK button is pressed, attempt to parse the genes from the text.</pre>
+                      <pre class="language-r">                     pre_output = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">405</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # This can be IDs and/or names of genes.</pre>
+                      <pre class="language-r">                     post_output = NULL) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">406</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">35</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Remove the modal and display notification message.</pre>
+                      <pre class="language-r">  logger::log_info("Initializing tm_g_pca")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">407</td>
+                    <td class="num">36</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(input$ok_button, {</pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">408</td>
+                    <td class="num">37</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_text &lt;- input$gene_text</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">409</td>
+                    <td class="num">38</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">39</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">410</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">411</td>
+                    <td class="num">41</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (!nzchar(gene_text)) {</pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">412</td>
+                    <td class="num">42</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">413</td>
+                    <td class="num">43</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Please enter at least one full gene ID.",</pre>
+                      <pre class="language-r">    server = srv_g_pca,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">414</td>
+                    <td class="num">44</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          type = "error"</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">415</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">45</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">46</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">416</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">417</td>
+                    <td class="num">48</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        words &lt;- h_extract_words(gene_text)</pre>
+                      <pre class="language-r">    ui = ui_g_pca,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">418</td>
+                    <td class="num">49</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        parse_result &lt;- h_parse_genes(words, choices = gene_choices)</pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">419</td>
+                    <td class="num">50</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(paste(</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">420</td>
+                    <td class="num">51</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Parsed total", nrow(parse_result), "genes from", length(words), "words"</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">421</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">52</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ))</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">422</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">53</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        parsed_genes(parse_result)</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">423</td>
+                    <td class="num">54</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        removeModal()</pre>
+                      <pre class="language-r">    datanames = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">424</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">425</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">426</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">427</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the gene choice is updated, then also set the names</pre>
+                      <pre class="language-r">#' @describeIn tm_g_pca sets up the user interface.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">428</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # correctly by looking up in current choices.</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">429</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">60</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    named_genes &lt;- eventReactive(input$genes, ignoreNULL = FALSE, {</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">430</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">61</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes &lt;- input$genes</pre>
+                      <pre class="language-r">ui_g_pca &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">431</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">62</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices &lt;- gene_choices()</pre>
+                      <pre class="language-r">                     data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">432</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">63</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ret &lt;- if (!is.null(genes)) {</pre>
+                      <pre class="language-r">                     mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">433</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        which_id &lt;- match(genes, gene_choices$id)</pre>
+                      <pre class="language-r">                     pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">434</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">65</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        gene_names &lt;- gene_choices$name[which_id]</pre>
+                      <pre class="language-r">                     post_output) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">435</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">66</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        stats::setNames(genes, gene_names)</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">436</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">67</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">  mae &lt;- data[[mae_name]]()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">437</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">68</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        NULL</pre>
+                      <pre class="language-r">  experiment_name_choices &lt;- names(mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">438</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">439</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">70</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ret</pre>
+                      <pre class="language-r">  tagList(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">440</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">71</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">    teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">441</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">72</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      include_css_files(pattern = "*"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">442</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">73</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    reactive({</pre>
+                      <pre class="language-r">      encoding = div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">443</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::gene_spec(</pre>
+                      <pre class="language-r">        ### Reporter</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">444</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        genes = named_genes(),</pre>
+                      <pre class="language-r">        teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">445</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">76</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        fun = funs[[input$fun_name]],</pre>
+                      <pre class="language-r">        ###</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">446</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">77</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        fun_name = input$fun_name</pre>
+                      <pre class="language-r">        tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">447</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">        helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">448</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">79</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">        experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">449</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">        assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">450</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">81</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">        conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">451</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">82</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          condition = "input.tab_selected == 'PCA'",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">452</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">83</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Validation of Gene Specification</pre>
+                      <pre class="language-r">          ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">453</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">84</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("color"), "Optional color variable"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">454</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">85</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">          selectizeInput(ns("x_var"), "Select X-axis PC", choices = ""),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">455</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">86</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          selectizeInput(ns("y_var"), "Select Y-axis PC", choices = "")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">456</td>
+                    <td class="num">87</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This validation function checks that a given [`hermes::GeneSpec`] has at least</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">457</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">88</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' one gene selected and that all genes are included in possible choices.</pre>
+                      <pre class="language-r">        teal.widgets::panel_group(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">89</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          teal.widgets::panel_item(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">458</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">90</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            input_id = "settings_item",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">459</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">91</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param gene_spec (`GeneSpec`)\cr gene specification.</pre>
+                      <pre class="language-r">            collapsed = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">460</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">92</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param gene_choices (`character`)\cr all possible gene choices.</pre>
+                      <pre class="language-r">            title = "Additional Settings",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">461</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">93</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            tags$label("Use only Top Variance Genes"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">462</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">94</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">            shinyWidgets::switchInput(ns("filter_top"), value = FALSE, size = "mini"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">463</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">95</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">validate_gene_spec &lt;- function(gene_spec,</pre>
+                      <pre class="language-r">            conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">464</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">96</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                               gene_choices) {</pre>
+                      <pre class="language-r">              condition = "input.filter_top",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">465</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">97</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_r6(gene_spec, "GeneSpec")</pre>
+                      <pre class="language-r">              ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">466</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">98</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(gene_choices)</pre>
+                      <pre class="language-r">              sliderInput(ns("n_top"), label = "Number of Top Genes", min = 10, max = 5000, value = 500)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">467</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">            ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">468</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">100</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  validate(need(</pre>
+                      <pre class="language-r">            conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">469</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">101</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    !is.null(gene_spec$get_genes()),</pre>
+                      <pre class="language-r">              condition = "input.tab_selected == 'PCA'",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">470</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">102</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "please select at least one gene"</pre>
+                      <pre class="language-r">              ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">471</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">103</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ))</pre>
+                      <pre class="language-r">              tags$label("Show Variance %"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">472</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">104</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  genes_not_included &lt;- setdiff(gene_spec$get_genes(), gene_choices)</pre>
+                      <pre class="language-r">              shinyWidgets::switchInput(ns("var_pct"), value = TRUE, size = "mini"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">473</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">105</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  n_not_incl &lt;- length(genes_not_included)</pre>
+                      <pre class="language-r">              tags$label("Show Label"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">474</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">106</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  validate(need(</pre>
+                      <pre class="language-r">              shinyWidgets::switchInput(ns("label"), value = TRUE, size = "mini")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">475</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">107</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    identical(n_not_incl, 0L),</pre>
+                      <pre class="language-r">            ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">476</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">108</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    paste(</pre>
+                      <pre class="language-r">            conditionalPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">477</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">109</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      n_not_incl,</pre>
+                      <pre class="language-r">              condition = "input.tab_selected == 'PC and Sample Correlation'",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">478</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">110</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ifelse(n_not_incl &gt; 1, "genes", "gene"),</pre>
+                      <pre class="language-r">              ns = ns,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">479</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">111</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::h_parens(hermes::h_short_list(genes_not_included)),</pre>
+                      <pre class="language-r">              tags$label("Cluster columns"),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">480</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">112</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "not included, please unlock or change filters"</pre>
+                      <pre class="language-r">              shinyWidgets::switchInput(ns("cluster_columns"), value = FALSE, size = "mini")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">481</td>
+                    <td class="num">113</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">            ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">482</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ))</pre>
+                      <pre class="language-r">            tags$label("View Matrix"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">483</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">115</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">            shinyWidgets::switchInput(ns("show_matrix"), value = TRUE, size = "mini")</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/quality.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">116</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Most Expressed Genes Plot</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">117</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">118</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">4</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">119</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      output = div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">120</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function plots the most expressed genes.</pre>
+                      <pre class="language-r">        style = "display:flow-root",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">121</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        tabsetPanel(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">122</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          id = ns("tab_selected"),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">123</td>
+                    <td class="coverage">1<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          type = "tabs",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">124</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams function_arguments</pre>
+                      <pre class="language-r">          tabPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">125</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">            "PCA",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">126</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Plot to be displayed in the teal app.</pre>
+                      <pre class="language-r">            column(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">127</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">              width = 12,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">128</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">              div(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                class = "my-5",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">130</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">                teal.widgets::plot_with_settings_ui(ns("plot_pca"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' library(hermes)</pre>
+                      <pre class="language-r">              ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">132</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' object &lt;- HermesData(summarized_experiment)</pre>
+                      <pre class="language-r">              DT::DTOutput(ns("table_pca"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">16</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' result &lt;- top_gene_plot(object, assay_name = "counts")</pre>
+                      <pre class="language-r">            )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">top_gene_plot &lt;- function(object, assay_name) {</pre>
+                      <pre class="language-r">          ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">18</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">135</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  top_gene &lt;- hermes::top_genes(</pre>
+                      <pre class="language-r">          tabPanel(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">19</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">136</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    object = object,</pre>
+                      <pre class="language-r">            "PC and Sample Correlation",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">20</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">137</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay_name = assay_name,</pre>
+                      <pre class="language-r">            column(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">21</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">138</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    summary_fun = rowMeans</pre>
+                      <pre class="language-r">              width = 12,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">139</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">              div(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">23</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">140</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hermes::autoplot(</pre>
+                      <pre class="language-r">                class = "my-5",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">24</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">141</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    top_gene,</pre>
+                      <pre class="language-r">                teal.widgets::plot_with_settings_ui(ns("plot_cor"))</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">25</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">142</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x_lab = "Gene",</pre>
+                      <pre class="language-r">              ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">26</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">143</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    y_lab = paste("Mean", assay_name, "across samples")</pre>
+                      <pre class="language-r">              DT::DTOutput(ns("table_cor"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">            )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Correlation Heatmap Plot</pre>
+                      <pre class="language-r">      ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">31</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">148</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">32</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">149</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This function plots the correlation heatmap.</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">153</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams function_arguments</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">154</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @describeIn tm_g_pca sets up the server with reactive graph.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">155</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Plot to be displayed in the teal app.</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">40</td>
+                    <td class="num">157</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">srv_g_pca &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">158</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                      data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">159</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">                      filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">160</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' library(hermes)</pre>
+                      <pre class="language-r">                      reporter,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">161</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' object &lt;- HermesData(summarized_experiment)</pre>
+                      <pre class="language-r">                      mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">162</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' result &lt;- heatmap_plot(object, assay_name = "counts")</pre>
+                      <pre class="language-r">                      exclude_assays) {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">163</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">164</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">165</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">166</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">heatmap_plot &lt;- function(object, assay_name) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">47</td>
+                    <td class="num">167</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  heatmap &lt;- hermes::correlate(</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">48</td>
+                    <td class="num">168</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    object = object,</pre>
+                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">49</td>
+                    <td class="num">169</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay_name = assay_name</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">50</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">51</td>
+                    <td class="num">170</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  hermes::autoplot(heatmap)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">52</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">53</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">171</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">54</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">172</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for RNA-seq Quality Control</pre>
+                      <pre class="language-r">      mae_name = mae_name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">173</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">56</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">174</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">57</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">175</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">58</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">176</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This module adds quality flags, filters by genes and/or samples,</pre>
+                      <pre class="language-r">      assays = experiment$assays,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">59</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">177</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' normalizes `AnyHermesData` objects and provides interactive plots</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">178</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' for RNA-seq gene expression quality control.</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">61</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">179</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    color &lt;- sampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">62</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">180</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      "color",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">63</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">181</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">64</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">182</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">      original_data = experiment$data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">183</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">184</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">185</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    # Total number of genes at the moment.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">68</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">186</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">    n_genes &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">69</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">187</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">70</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">188</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">      nrow(experiment_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">189</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">190</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">191</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">    # When the total number changes or gene filter is activated, update slider max.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">74</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">192</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules(</pre>
+                      <pre class="language-r">    observeEvent(list(n_genes(), input$filter_top), {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">75</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">193</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     tm_g_quality(</pre>
+                      <pre class="language-r">      n_genes &lt;- n_genes()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">76</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">194</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       label = "Quality Control",</pre>
+                      <pre class="language-r">      filter_top &lt;- input$filter_top</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">77</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">195</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">      if (filter_top) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">78</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">196</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">        n_top &lt;- input$n_top</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">79</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">197</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">        updateSliderInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">80</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">198</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">          session = session,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">81</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">199</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">          inputId = "n_top",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">82</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">200</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">          value = min(n_top, n_genes),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">83</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">201</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">          max = n_genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">84</td>
+                    <td class="num">202</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_quality &lt;- function(label,</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">85</td>
+                    <td class="num">203</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         mae_name,</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">86</td>
+                    <td class="num">204</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         exclude_assays = character(),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">87</td>
+                    <td class="num">205</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         pre_output = NULL,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">88</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         post_output = NULL) {</pre>
+                      <pre class="language-r">    # When the chosen experiment or assay name changes, recompute the PC.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">89</td>
+                    <td class="num">207</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">    pca_result &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">90</td>
+                    <td class="num">208</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">91</td>
+                    <td class="num">209</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
+                      <pre class="language-r">      filter_top &lt;- input$filter_top</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">92</td>
+                    <td class="num">210</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">      n_top &lt;- input$n_top</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">93</td>
+                    <td class="num">211</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">      assay_name &lt;- assay()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">94</td>
+                    <td class="num">212</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">95</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">96</td>
+                    <td class="num">213</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
+                      <pre class="language-r">      validate(need(hermes::is_hermes_data(experiment_data), "please use HermesData() on input experiments"))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">97</td>
+                    <td class="num">214</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_quality,</pre>
+                      <pre class="language-r">      req(isTRUE(assay_name %in% SummarizedExperiment::assayNames(experiment_data)))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">98</td>
+                    <td class="num">215</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">99</td>
+                    <td class="num">216</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">        ncol(experiment_data) &gt; 2,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">100</td>
+                    <td class="num">217</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">        "Sample size is too small. PCA needs more than 2 samples."</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">101</td>
+                    <td class="num">218</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">102</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_quality,</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">103</td>
+                    <td class="num">219</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">104</td>
+                    <td class="num">220</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">        nrow(experiment_data) &gt; 1,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">105</td>
+                    <td class="num">221</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">        "Number of genes is too small. PCA needs more than 1 gene."</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">106</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">222</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">108</td>
+                    <td class="num">224</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = mae_name</pre>
+                      <pre class="language-r">      hermes::calc_pca(experiment_data, assay_name, n_top = if (filter_top) n_top else NULL)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">225</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">226</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">227</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    # When experiment or assay name changes, update choices for PCs in x_var and y_var.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">112</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">228</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_quality sets up the user interface.</pre>
+                      <pre class="language-r">    observeEvent(pca_result(), {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">113</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">229</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      pca_result_x &lt;- pca_result()$x</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">114</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">230</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      pc_choices &lt;- seq_len(ncol(pca_result_x))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">115</td>
+                    <td class="num">231</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ui_g_quality &lt;- function(id,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">116</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">232</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         data,</pre>
+                      <pre class="language-r">      id_names &lt;- c("x_var", "y_var")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">117</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">233</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         mae_name,</pre>
+                      <pre class="language-r">      for (i in seq_along(id_names)) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">118</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">234</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         pre_output,</pre>
+                      <pre class="language-r">        updateSelectizeInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">119</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">235</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         post_output) {</pre>
+                      <pre class="language-r">          session,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">120</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">236</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">          id_names[i],</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">121</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">237</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">          choices = pc_choices,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">122</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">238</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    encoding = div(</pre>
+                      <pre class="language-r">          selected = pc_choices[i]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">123</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ### Reporter</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">124</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ###</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">126</td>
-                    <td class="coverage">1<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">127</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">241</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">128</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">242</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">129</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">243</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      selectInput(</pre>
+                      <pre class="language-r">    # Compute correlation of PC with sample variables.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">130</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">244</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns("plot_type"),</pre>
+                      <pre class="language-r">    cor_result &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">131</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">245</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Plot Type",</pre>
+                      <pre class="language-r">      pca_result &lt;- pca_result()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">132</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">246</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = c(</pre>
+                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">133</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">247</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Histogram",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">134</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">248</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Q-Q Plot",</pre>
+                      <pre class="language-r">      hermes::correlate(pca_result, experiment_data)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">135</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">249</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Density",</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">136</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">250</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Boxplot",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">137</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">251</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Top Genes Plot",</pre>
+                      <pre class="language-r">    # Compute &amp; display PCA matrix table if show_matrix is TRUE.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">138</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">252</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Correlation Heatmap"</pre>
+                      <pre class="language-r">    show_matrix_pca &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">139</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">253</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      if (input$show_matrix) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">140</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">254</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">        pca_result_x &lt;- pca_result()$x</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">141</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">255</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conditionalPanel(</pre>
+                      <pre class="language-r">        pca_result_x &lt;- round(pca_result_x, 3)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">142</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">256</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        condition = "input.plot_type == 'Top Genes Plot' || input.plot_type == 'Correlation Heatmap'",</pre>
+                      <pre class="language-r">        as.data.frame(pca_result_x)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">143</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">257</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns = ns,</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">144</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">258</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assaySpecInput(ns("assay"))</pre>
+                      <pre class="language-r">        NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">145</td>
+                    <td class="num">259</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">146</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">260</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Gene Filter Settings", class = "text-primary"),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">147</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">261</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      shinyWidgets::switchInput(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">148</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">262</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns("filter_gene"),</pre>
+                      <pre class="language-r">    output$table_pca &lt;- DT::renderDT({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">149</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">263</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        value = TRUE,</pre>
+                      <pre class="language-r">      show_matrix_pca &lt;- show_matrix_pca()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">150</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">264</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        size = "mini"</pre>
+                      <pre class="language-r">      DT::datatable(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">151</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">265</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">        show_matrix_pca,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">152</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">266</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conditionalPanel(</pre>
+                      <pre class="language-r">        rownames = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">153</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">267</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        condition = "input.filter_gene",</pre>
+                      <pre class="language-r">        options = list(scrollX = TRUE, pageLength = 30, lengthMenu = c(5, 15, 30, 100)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">154</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">268</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns = ns,</pre>
+                      <pre class="language-r">        caption = "PCA Matrix"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">155</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">269</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        sliderInput(ns("min_cpm"), label = ("Minimum CPM"), min = 1, max = 10, value = 5),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">156</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">270</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        sliderInput(ns("min_cpm_prop"), label = ("Minimum CPM Proportion"), min = 0.01, max = 0.99, value = 0.25),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">157</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">271</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::optionalSelectInput(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">158</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">272</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns("annotate"),</pre>
+                      <pre class="language-r">    # Compute &amp; display correlation matrix if show_matrix is TRUE</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">159</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">273</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          label = "Required Annotations",</pre>
+                      <pre class="language-r">    show_matrix_cor &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">160</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">274</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = "",</pre>
+                      <pre class="language-r">      if (input$show_matrix) {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">161</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">275</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = "",</pre>
+                      <pre class="language-r">        cor_result &lt;- cor_result()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">162</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">276</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          multiple = TRUE</pre>
+                      <pre class="language-r">        cor_result &lt;- round(cor_result, 3)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">163</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">277</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">        as.data.frame(cor_result)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">164</td>
+                    <td class="num">278</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">      } else {</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">165</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">279</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Sample Filter Settings", class = "text-primary"),</pre>
+                      <pre class="language-r">        NULL</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">166</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">280</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      shinyWidgets::switchInput(</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">167</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">281</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns("filter_sample"),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">168</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">282</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        value = TRUE,</pre>
+                      <pre class="language-r">    output$table_cor &lt;- DT::renderDT({</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">169</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">283</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        size = "mini"</pre>
+                      <pre class="language-r">      show_matrix_cor &lt;- show_matrix_cor()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">170</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">284</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ),</pre>
+                      <pre class="language-r">      DT::datatable(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">171</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">285</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      conditionalPanel(</pre>
+                      <pre class="language-r">        show_matrix_cor,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">172</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">286</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        condition = "input.filter_sample",</pre>
+                      <pre class="language-r">        rownames = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">173</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">287</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ns = ns,</pre>
+                      <pre class="language-r">        options = list(scrollX = TRUE, pageLength = 30, lengthMenu = c(5, 15, 30, 100)),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">174</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">288</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        sliderInput(ns("min_corr"), label = ("Minimum Correlation"), min = 0.01, max = 0.99, value = 0.5),</pre>
+                      <pre class="language-r">        caption = "PC and Sample Correlation Matrix"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">175</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">289</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        radioButtons(</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">176</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">290</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns("min_depth"),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">177</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">291</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          label = "Minimum Depth",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">178</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">292</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          choices = c("Default", "Specify"),</pre>
+                      <pre class="language-r">    # Render plot PCA output.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">179</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">293</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          selected = "Default"</pre>
+                      <pre class="language-r">    plot_pca &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">180</td>
+                    <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ),</pre>
+                      <pre class="language-r">      # Resolve all reactivity.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">181</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">295</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        conditionalPanel(</pre>
+                      <pre class="language-r">      pca_result &lt;- pca_result()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">182</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">296</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          condition = "input.min_depth == 'Specify'",</pre>
+                      <pre class="language-r">      experiment_data &lt;- color$experiment_data()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">183</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">297</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          ns = ns,</pre>
+                      <pre class="language-r">      x_var &lt;- as.numeric(input$x_var)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">184</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">298</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sliderInput(ns("min_depth_continuous"), label = NULL, min = 1, max = 10, value = 1)</pre>
+                      <pre class="language-r">      y_var &lt;- as.numeric(input$y_var)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">185</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">299</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">      data &lt;- as.data.frame(SummarizedExperiment::colData(color$experiment_data()))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">186</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">300</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">      color_var &lt;- color$sample_var()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">187</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">301</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">      assay_name &lt;- assay()</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">188</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">302</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                      <pre class="language-r">      var_pct &lt;- input$var_pct</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">189</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">303</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pre_output = pre_output,</pre>
+                      <pre class="language-r">      label &lt;- input$label</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">190</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">304</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    post_output = post_output</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">191</td>
+                    <td class="num">305</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">      # Require which states need to be truthy.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">192</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">306</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      req(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">193</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">307</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        assay_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">194</td>
+                    <td class="num">308</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_quality sets up the server with reactive graphs.</pre>
+                      <pre class="language-r">        # Note: The following statements are important to make sure the UI inputs have been updated.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">195</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">309</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">        isTRUE(assay_name %in% SummarizedExperiment::assayNames(experiment_data)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">196</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">310</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">        is.null(color_var) || isTRUE(color_var %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">311</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        cancelOutput = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">197</td>
+                    <td class="num">312</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_quality &lt;- function(id,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">198</td>
+                    <td class="num">313</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          data,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">199</td>
+                    <td class="num">314</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          filter_panel_api,</pre>
+                      <pre class="language-r">      # Validate and give useful messages to the user. Note: no need to duplicate here req() from above.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">200</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">315</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          reporter,</pre>
+                      <pre class="language-r">      validate(need(x_var != y_var, "please select two different principal components"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">201</td>
+                    <td class="num">316</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          mae_name,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">202</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">317</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          exclude_assays) {</pre>
+                      <pre class="language-r">      hermes::autoplot(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">203</td>
+                    <td class="num">318</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">        object = pca_result,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">204</td>
+                    <td class="num">319</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">        assay_name = assay_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">205</td>
+                    <td class="num">320</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">        x = x_var,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">206</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">321</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        y = y_var,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">207</td>
+                    <td class="num">322</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">        data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">208</td>
+                    <td class="num">323</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">        colour = color_var,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">209</td>
+                    <td class="num">324</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">        variance_percentage = var_pct,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">210</td>
+                    <td class="num">325</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">        label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">211</td>
+                    <td class="num">326</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">        label.repel = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">212</td>
+                    <td class="num">327</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name</pre>
+                      <pre class="language-r">        label.show.legend = FALSE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">213</td>
+                    <td class="num">328</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">214</td>
+                    <td class="num">329</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">215</td>
+                    <td class="num">330</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">    output$plot_pca &lt;- renderPlot(plot_pca())</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">216</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">331</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">217</td>
+                    <td class="num">332</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = reactive({</pre>
+                      <pre class="language-r">    pws_pca &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">218</td>
+                    <td class="num">333</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        union(</pre>
+                      <pre class="language-r">      id = "plot_pca",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">219</td>
+                    <td class="num">334</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          experiment$assays(),</pre>
+                      <pre class="language-r">      plot_r = plot_pca</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">220</td>
+                    <td class="num">335</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          # Add all the additional normalized assays.</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">221</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">          c("cpm", "rpkm", "tpm", "voom", "vst")</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">222</td>
+                    <td class="num">336</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">337</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }),</pre>
+                      <pre class="language-r">    # render correlation heatmap</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">224</td>
+                    <td class="num">338</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">225</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    plot_cor &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">226</td>
+                    <td class="num">339</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      # Resolve all reactivity.</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">227</td>
+                    <td class="num">340</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment_properties &lt;- eventReactive(experiment$name(), {</pre>
+                      <pre class="language-r">      cor_result &lt;- cor_result()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">228</td>
+                    <td class="num">341</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data &lt;- experiment$data()</pre>
+                      <pre class="language-r">      cluster_columns &lt;- input$cluster_columns</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">229</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">342</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      cpm &lt;- edgeR::cpm(hermes::counts(data))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">230</td>
+                    <td class="num">343</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      depth &lt;- colSums(hermes::counts(data))</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">231</td>
+                    <td class="num">344</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      list(</pre>
+                      <pre class="language-r">        !any(is.na(cor_result)),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">232</td>
+                    <td class="num">345</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        annotations = names(hermes::annotation(data)),</pre>
+                      <pre class="language-r">        "Obtained NA results in the correlation matrix, therefore no plot can be produced"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">233</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">346</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_cpm_calc = floor(min(cpm)),</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">234</td>
+                    <td class="num">347</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        max_cpm_calc = floor(max(cpm)),</pre>
+                      <pre class="language-r">      hermes::autoplot(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">235</td>
+                    <td class="num">348</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_depth_calc = min(depth),</pre>
+                      <pre class="language-r">        object = cor_result,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">236</td>
+                    <td class="num">349</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        max_depth_calc = max(depth)</pre>
+                      <pre class="language-r">        cluster_columns = cluster_columns</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">237</td>
+                    <td class="num">350</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">238</td>
+                    <td class="num">351</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">239</td>
+                    <td class="num">352</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">240</td>
+                    <td class="num">353</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(experiment_properties(), {</pre>
+                      <pre class="language-r">    pws_cor &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">241</td>
+                    <td class="num">354</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      properties &lt;- experiment_properties()</pre>
+                      <pre class="language-r">      id = "plot_cor",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">355</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      plot_r = plot_cor</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">242</td>
+                    <td class="num">356</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    )</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">357</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
+                  <tr class="never">
+                    <td class="num">358</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ### REPORTER</pre>
+                    </td>
+                  </tr>
                   <tr class="missed">
-                    <td class="num">243</td>
+                    <td class="num">359</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::updateOptionalSelectInput(</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">244</td>
+                    <td class="num">360</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        session,</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">245</td>
+                    <td class="num">361</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "annotate",</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">246</td>
+                    <td class="num">362</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        choices = properties$annotations,</pre>
+                      <pre class="language-r">          title = "PCA",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">247</td>
+                    <td class="num">363</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        selected = "WidthBP"</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">248</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">364</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">249</td>
+                    <td class="num">365</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      updateSliderInput(</pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">366</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">250</td>
+                    <td class="num">367</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        session,</pre>
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">251</td>
+                    <td class="num">368</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "min_cpm",</pre>
+                      <pre class="language-r">        if (input$tab_selected == "PCA") {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">252</td>
+                    <td class="num">369</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min = properties$min_cpm_calc,</pre>
+                      <pre class="language-r">          encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">253</td>
+                    <td class="num">370</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        max = properties$max_cpm_calc,</pre>
+                      <pre class="language-r">            "Experiment:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">254</td>
+                    <td class="num">371</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        value = properties$min_cpm_calc</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">255</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">            input$`experiment-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">256</td>
+                    <td class="num">372</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      updateSliderInput(</pre>
+                      <pre class="language-r">            "\nAssay:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">257</td>
+                    <td class="num">373</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        session,</pre>
+                      <pre class="language-r">            input$`assay-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">258</td>
+                    <td class="num">374</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "min_depth_continuous",</pre>
+                      <pre class="language-r">            "\nOptional Color Variable:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">259</td>
+                    <td class="num">375</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min = properties$min_depth_calc,</pre>
+                      <pre class="language-r">            input$`color-sample_var`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">260</td>
+                    <td class="num">376</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        max = properties$max_depth_calc,</pre>
+                      <pre class="language-r">            "\nX-axis PC:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">261</td>
+                    <td class="num">377</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        value = properties$min_depth_calc</pre>
+                      <pre class="language-r">            input$x_var,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">262</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">378</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">            "\nY-axis PC:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">263</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">379</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">            input$y_var,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">264</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">380</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">            "\nUse Top Variance Genes:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">265</td>
+                    <td class="num">381</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    min_depth_final &lt;- reactive({</pre>
+                      <pre class="language-r">            input$filter_top,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">266</td>
+                    <td class="num">382</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      min_depth &lt;- input$min_depth</pre>
+                      <pre class="language-r">            "\nNumber of Top Genes:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">267</td>
+                    <td class="num">383</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      min_depth_continuous &lt;- input$min_depth_continuous</pre>
+                      <pre class="language-r">            input$n_top,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">268</td>
+                    <td class="num">384</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (min_depth == "Specify") {</pre>
+                      <pre class="language-r">            "\nShow Variance %:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">269</td>
+                    <td class="num">385</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        req(min_depth_continuous)</pre>
+                      <pre class="language-r">            input$var_pct,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">270</td>
+                    <td class="num">386</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_depth_continuous</pre>
+                      <pre class="language-r">            "\nShow Matrix:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">271</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">387</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">            input$show_matrix,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">272</td>
+                    <td class="num">388</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        NULL</pre>
+                      <pre class="language-r">            "\nShow Label:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">273</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">389</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">            input$label</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">274</td>
+                    <td class="num">390</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">275</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">391</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">276</td>
+                    <td class="num">392</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    control &lt;- reactive({</pre>
+                      <pre class="language-r">          final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">277</td>
+                    <td class="num">393</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      min_cpm &lt;- input$min_cpm</pre>
+                      <pre class="language-r">            null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">278</td>
+                    <td class="num">394</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      min_cpm_prop &lt;- input$min_cpm_prop</pre>
+                      <pre class="language-r">            paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">279</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">395</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      min_corr &lt;- input$min_corr</pre>
+                      <pre class="language-r">          } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">280</td>
+                    <td class="num">396</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      min_depth_final &lt;- min_depth_final()</pre>
+                      <pre class="language-r">            paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">281</td>
+                    <td class="num">397</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">282</td>
+                    <td class="num">398</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">          card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">283</td>
+                    <td class="num">399</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_cpm,</pre>
+                      <pre class="language-r">          card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">284</td>
+                    <td class="num">400</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_cpm_prop,</pre>
+                      <pre class="language-r">          card$append_plot(plot_pca(), dim = pws_pca$dim())</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">285</td>
+                    <td class="num">401</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_corr</pre>
+                      <pre class="language-r">          card$append_text("Table", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">286</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">402</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">          card$append_table(show_matrix_pca())</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">287</td>
+                    <td class="num">403</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">288</td>
+                    <td class="num">404</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::control_quality(</pre>
+                      <pre class="language-r">          encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">289</td>
+                    <td class="num">405</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_cpm = min_cpm,</pre>
+                      <pre class="language-r">            "Experiment:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">290</td>
+                    <td class="num">406</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_cpm_prop = min_cpm_prop,</pre>
+                      <pre class="language-r">            input$`experiment-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">291</td>
+                    <td class="num">407</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_corr = min_corr,</pre>
+                      <pre class="language-r">            "\nAssay:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">292</td>
+                    <td class="num">408</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        min_depth = min_depth_final</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">293</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">294</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">295</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">            input$`assay-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">296</td>
+                    <td class="num">409</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    object_flagged &lt;- reactive({</pre>
+                      <pre class="language-r">            "\nUse Top Variance Genes:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">297</td>
+                    <td class="num">410</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      control &lt;- control()</pre>
+                      <pre class="language-r">            input$filter_top,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">298</td>
+                    <td class="num">411</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      object &lt;- experiment$data()</pre>
+                      <pre class="language-r">            "\nNumber of Top Genes:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">299</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">412</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">            input$top_n,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">300</td>
+                    <td class="num">413</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      already_added &lt;- ("control_quality_flags" %in% names(hermes::metadata(object)))</pre>
+                      <pre class="language-r">            "\nCluster Columns:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">301</td>
+                    <td class="num">414</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(!already_added, "Quality flags have already been added to this experiment"))</pre>
+                      <pre class="language-r">            paste0(input$cluster_columns, collapse = ", "),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">302</td>
+                    <td class="num">415</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (any(c("cpm", "rpkm", "tpm", "voom", "vst") %in% SummarizedExperiment::assayNames(object))) {</pre>
+                      <pre class="language-r">            "\nShow Matrix:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">303</td>
+                    <td class="num">416</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification("Original normalized assays will be overwritten", type = "warning")</pre>
+                      <pre class="language-r">            input$show_matrix</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">304</td>
+                    <td class="num">417</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">305</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">418</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">306</td>
+                    <td class="num">419</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::add_quality_flags(</pre>
+                      <pre class="language-r">          final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">307</td>
+                    <td class="num">420</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object,</pre>
+                      <pre class="language-r">            null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">308</td>
+                    <td class="num">421</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        control = control</pre>
+                      <pre class="language-r">            paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">309</td>
+                    <td class="num">422</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">          } else {</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">423</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">            paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">310</td>
+                    <td class="num">424</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">          }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">311</td>
+                    <td class="num">425</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">312</td>
+                    <td class="num">426</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    object_final &lt;- reactive({</pre>
+                      <pre class="language-r">          card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">313</td>
+                    <td class="num">427</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      object_flagged &lt;- object_flagged()</pre>
+                      <pre class="language-r">          card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">314</td>
+                    <td class="num">428</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter &lt;- input$filter</pre>
+                      <pre class="language-r">          card$append_plot(plot_cor())</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">315</td>
+                    <td class="num">429</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      annotate &lt;- input$annotate</pre>
+                      <pre class="language-r">          card$append_plot(plot_cor(), dim = pws_cor$dim())</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">316</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">430</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          card$append_text("Table", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">317</td>
+                    <td class="num">431</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(!is_blank(annotate))</pre>
+                      <pre class="language-r">          card$append_table(show_matrix_cor())</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">318</td>
+                    <td class="num">432</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">319</td>
+                    <td class="num">433</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      result &lt;- hermes::filter(</pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">320</td>
+                    <td class="num">434</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object_flagged,</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">321</td>
+                    <td class="num">435</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        what = filter,</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">322</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">436</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        annotation_required = annotate</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">323</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">437</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">        card</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">324</td>
+                    <td class="num">438</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">325</td>
+                    <td class="num">439</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">326</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">440</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        nrow(result) &gt;= 2,</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">327</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">441</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Please change gene filters to ensure that there are at least 2 genes"</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">328</td>
+                    <td class="num">442</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">329</td>
+                    <td class="num">443</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">330</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">444</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::normalize(result)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">331</td>
+                    <td class="num">445</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @describeIn tm_g_pca sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">332</td>
+                    <td class="num">446</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">333</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">447</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">334</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">448</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      object_final &lt;- object_final()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">335</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">449</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_type &lt;- input$plot_type</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">336</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">450</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay_name &lt;- assay()</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">337</td>
+                    <td class="num">451</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   sample_tm_g_pca()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">338</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">452</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      switch(plot_type,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">339</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">453</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Histogram" = hermes::draw_libsize_hist(object_final),</pre>
+                      <pre class="language-r">sample_tm_g_pca &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">340</td>
+                    <td class="num">454</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Density" = hermes::draw_libsize_densities(object_final),</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">341</td>
+                    <td class="num">455</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Q-Q Plot" = hermes::draw_libsize_qq(object_final),</pre>
+                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">342</td>
+                    <td class="num">456</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Boxplot" = hermes::draw_nonzero_boxplot(object_final),</pre>
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">343</td>
+                    <td class="num">457</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Top Genes Plot" = top_gene_plot(object_final, assay_name = assay_name),</pre>
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">344</td>
+                    <td class="num">458</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Correlation Heatmap" = heatmap_plot(object_final, assay_name = assay_name)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">345</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">346</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">347</td>
+                    <td class="num">459</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">348</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    modules = teal::modules(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">349</td>
+                    <td class="num">460</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">      tm_g_pca(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">350</td>
+                    <td class="num">461</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot",</pre>
+                      <pre class="language-r">        label = "pca",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">351</td>
+                    <td class="num">462</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = plot_r</pre>
+                      <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">352</td>
+                    <td class="num">463</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">353</td>
+                    <td class="num">464</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">354</td>
+                    <td class="num">465</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
-                    </td>
-                  </tr>
-                  <tr class="missed">
-                    <td class="num">355</td>
-                    <td class="coverage">!</td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">356</td>
+                    <td class="num">466</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">357</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">467</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">358</td>
-                    <td class="coverage">!</td>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/utils.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
+                  <tr class="never">
+                    <td class="num">1</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Quality Control Plot")</pre>
+                      <pre class="language-r">#' Checking for Empty String</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">359</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">2</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Quality Control Plot", "header2")</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">360</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">3</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(tools::toTitleCase(input$plot_type), "header3")</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge('experimental')`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">361</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">4</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">362</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">5</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r">#' This predicate function is helpful for functions where arguments could</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">363</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">6</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                      <pre class="language-r">#' not yet be initialized from the teal module.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">364</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">7</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Experiment:",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">365</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">8</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`experiment-name`,</pre>
+                      <pre class="language-r">#' @param x object to check.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">366</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">9</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nPlot Type:",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">367</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">10</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$plot_type,</pre>
+                      <pre class="language-r">#' @return Flag whether `x` is identical to an empty string, i.e. `""`.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">368</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">11</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAssay:",</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">369</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">12</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`assay-name`,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">370</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">13</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nShow Gene Filter Settings:",</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">371</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">14</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$filter_gene,</pre>
+                      <pre class="language-r">#' is_blank("")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">372</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">15</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nMinimum CPM:",</pre>
+                      <pre class="language-r">#' is_blank(" ")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">373</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">16</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$min_cpm,</pre>
+                      <pre class="language-r">is_blank &lt;- function(x) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">374</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">17</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nMinimum CPM Proportion:",</pre>
+                      <pre class="language-r">  identical(x, "")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">375</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">18</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$min_cpm_prop,</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">376</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">19</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nRequired Annotations:",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">377</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">20</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(input$annotate, collapse = ", "),</pre>
+                      <pre class="language-r">#' Helper Function to Extract Words</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">378</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">21</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nShow Sample Filter Settings:",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">379</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">22</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$filter_sample,</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">380</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">23</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nMinimum Correlation:",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">381</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">24</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$min_corr,</pre>
+                      <pre class="language-r">#' This helper function extracts words from a string. Here words are defined</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">382</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">25</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nMinimum Depth:",</pre>
+                      <pre class="language-r">#' as containing lower or upper case letters, colons and dots. All other</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">383</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">26</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$min_depth,</pre>
+                      <pre class="language-r">#' characters are considered separators.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">384</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nMinimum Depth Value:",</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">385</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$min_depth_continuous</pre>
+                      <pre class="language-r">#' @param x (`string`)\cr input.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">386</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">387</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">#' @return Character vector with the extracted words.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">388</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">31</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">389</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">390</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">33</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">391</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">#' h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">392</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">35</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">#' h_extract_words("GeneID:1820, sdf.393; 32596")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">393</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">h_extract_words &lt;- function(x) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">394</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">37</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_string(x, min.chars = 1L)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">395</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">38</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">  stringr::str_extract_all(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">396</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">39</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">    x,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">397</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">40</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
+                      <pre class="language-r">    "[a-zA-Z0-9:\\.]+"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">398</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">41</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">  )[[1]]</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">399</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">42</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">400</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">43</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">401</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">#' Include `CSS` files from `/inst/css/` package directory to application header</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">402</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">45</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">403</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' `system.file` should not be used to access files in other packages, it does</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">404</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">47</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
+                      <pre class="language-r">#' not work with `devtools`. Therefore, we redefine this method in each package</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">405</td>
+                    <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">#' as needed. Thus, we do not export this method</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">406</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">407</td>
+                    <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">#' @param pattern (`character`) pattern of files to be included</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">408</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">409</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return HTML code that includes `CSS` files</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">410</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_quality sample module function.</pre>
+                      <pre class="language-r">#' @keywords internal</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">411</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">include_css_files &lt;- function(pattern = "*") { # nolint</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">55</td>
+                    <td class="coverage">12<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  css_files &lt;- list.files(</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">56</td>
+                    <td class="coverage">12<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    system.file("css", package = "teal.modules.hermes", mustWork = TRUE),</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">57</td>
+                    <td class="coverage">12<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    pattern = pattern, full.names = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">412</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">  )</pre>
+                    </td>
+                  </tr>
+                  <tr class="covered">
+                    <td class="num">59</td>
+                    <td class="coverage">12<em>x</em></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  return(shiny::singleton(shiny::tags$head(lapply(css_files, includeCSS))))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">413</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">414</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">415</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">#' Include `JS` files from `/inst/js/` package directory to application header</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">416</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_quality()</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">417</td>
+                    <td class="num">64</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' `system.file` should not be used to access files in other packages, it does</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">418</td>
+                    <td class="num">65</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_quality &lt;- function() {</pre>
+                      <pre class="language-r">#' not work with `devtools`. Therefore, we redefine this method in each package</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">419</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">#' as needed. Thus, we do not export this method</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">420</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">67</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">421</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">68</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
+                      <pre class="language-r">#' @param pattern (`character`) pattern of files to be included, passed to `system.file`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">422</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">69</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                      <pre class="language-r">#' @param except (`character`) vector of basename filenames to be excluded</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">423</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">70</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">424</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">71</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = teal::modules(</pre>
+                      <pre class="language-r">#' @return HTML code that includes `JS` files</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">425</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">72</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tm_g_quality(</pre>
+                      <pre class="language-r">#' @keywords internal</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">426</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">73</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = "quality",</pre>
+                      <pre class="language-r">include_js_files &lt;- function(pattern = "*") { # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">427</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">74</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae_name = "MAE"</pre>
+                      <pre class="language-r">  js_files &lt;- list.files(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">428</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">75</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    system.file("js", package = "teal.modules.hermes", mustWork = TRUE),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">429</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">76</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    pattern = pattern, full.names = TRUE</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">430</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">431</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">78</td>
+                    <td class="coverage">12<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">  return(singleton(lapply(js_files, includeScript)))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">432</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
@@ -25757,473 +25847,487 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">193</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">194</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">195</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Barplot")</pre>
+                      <pre class="language-r">          title = "Barplot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">196</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Barplot", "header2")</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">197</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">198</td>
                     <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">199</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">200</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">199</td>
+                    <td class="num">201</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">200</td>
+                    <td class="num">202</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "Experiment:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">201</td>
+                    <td class="num">203</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          input$`experiment-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">202</td>
+                    <td class="num">204</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "\nAssay:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">203</td>
+                    <td class="num">205</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          input$`assay-name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">204</td>
+                    <td class="num">206</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "\nFacetting Variable:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">205</td>
+                    <td class="num">207</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          input$`facet-sample_var`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">206</td>
+                    <td class="num">208</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "\nGenes Selected:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">207</td>
+                    <td class="num">209</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          paste0(x()$get_gene_labels(), collapse = ", "),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">208</td>
+                    <td class="num">210</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "\nGene Summary:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">209</td>
+                    <td class="num">211</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          input$`x-fun_name`,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">210</td>
+                    <td class="num">212</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "\nQuantiles:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">211</td>
+                    <td class="num">213</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          paste0(input$percentiles, collapse = ", "),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">212</td>
+                    <td class="num">214</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          "\nOptional Fill Variable:",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">213</td>
+                    <td class="num">215</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          input$`fill-sample_var`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">214</td>
+                    <td class="num">216</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">215</td>
+                    <td class="num">217</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">216</td>
+                    <td class="num">218</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">217</td>
+                    <td class="num">219</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">218</td>
+                    <td class="num">220</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">219</td>
+                    <td class="num">221</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">220</td>
+                    <td class="num">222</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">221</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">222</td>
+                    <td class="num">224</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">223</td>
+                    <td class="num">225</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">224</td>
+                    <td class="num">226</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">225</td>
+                    <td class="num">227</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">226</td>
+                    <td class="num">228</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">227</td>
+                    <td class="num">229</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">228</td>
+                    <td class="num">230</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">229</td>
+                    <td class="num">231</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">230</td>
+                    <td class="num">232</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        card</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">231</td>
+                    <td class="num">233</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">232</td>
+                    <td class="num">234</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">233</td>
+                    <td class="num">235</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">234</td>
+                    <td class="num">236</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">235</td>
+                    <td class="num">237</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">236</td>
+                    <td class="num">238</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">237</td>
+                    <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">238</td>
+                    <td class="num">240</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @describeIn tm_g_barplot sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">239</td>
+                    <td class="num">241</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">240</td>
+                    <td class="num">242</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">241</td>
+                    <td class="num">243</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">242</td>
+                    <td class="num">244</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">243</td>
+                    <td class="num">245</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">244</td>
+                    <td class="num">246</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'   sample_tm_g_barplot()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">245</td>
+                    <td class="num">247</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">246</td>
+                    <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">sample_tm_g_barplot &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">247</td>
+                    <td class="num">249</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">248</td>
+                    <td class="num">250</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">249</td>
+                    <td class="num">251</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">250</td>
+                    <td class="num">252</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">251</td>
+                    <td class="num">253</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">252</td>
+                    <td class="num">254</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">    modules = teal::modules(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">253</td>
+                    <td class="num">255</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">      tm_g_barplot(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">254</td>
+                    <td class="num">256</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        label = "barplot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">255</td>
+                    <td class="num">257</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">256</td>
+                    <td class="num">258</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">257</td>
+                    <td class="num">259</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">258</td>
+                    <td class="num">260</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">259</td>
+                    <td class="num">261</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
                       <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">260</td>
+                    <td class="num">262</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
@@ -26232,14 +26336,14 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                 </tbody>
               </table>
             </div>
-            <div id="R/boxplot.R" class="hidden">
+            <div id="R/forestplot.R" class="hidden">
               <table class="table-condensed">
                 <tbody>
                   <tr class="never">
                     <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Teal Module for RNA-seq Boxplot</pre>
+                      <pre class="language-r">#' Teal Module for Survival Forest Plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -26267,147 +26371,147 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This module provides an interactive boxplot for RNA-seq gene expression</pre>
+                      <pre class="language-r">#' This module provides an interactive survival forest plot.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' analysis.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">#' adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' mae_data &lt;- dataset("MAE", mae)</pre>
+                      <pre class="language-r">#'   dplyr::mutate(is_event = (.data$CNSR == 0))</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' app &lt;- init(</pre>
+                      <pre class="language-r">#' data &lt;- teal_data(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data = data,</pre>
+                      <pre class="language-r">#'   dataset(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   modules = modules(</pre>
+                      <pre class="language-r">#'     "ADTTE",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     tm_g_boxplot(</pre>
+                      <pre class="language-r">#'     adtte,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       label = "boxplot",</pre>
+                      <pre class="language-r">#'     code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">#'       dplyr::mutate(is_event = (.data$CNSR == 0))"</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">#'   ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">#'   dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -26421,1372 +26525,1372 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#'   modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">tm_g_boxplot &lt;- function(label,</pre>
+                      <pre class="language-r">#'     tm_g_forest_tte(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         mae_name,</pre>
+                      <pre class="language-r">#'       label = "forestplot",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         exclude_assays = character(),</pre>
+                      <pre class="language-r">#'       adtte_name = "ADTTE",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         summary_funs = list(</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           None = NULL,</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           Mean = colMeans,</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           Median = matrixStats::colMedians,</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           Max = matrixStats::colMaxs</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         ),</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         pre_output = NULL,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         post_output = NULL) {</pre>
+                      <pre class="language-r">tm_g_forest_tte &lt;- function(label,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">41</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  logger::log_info("Initializing tm_g_boxplot")</pre>
+                      <pre class="language-r">                            adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">42</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label)</pre>
+                      <pre class="language-r">                            mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">43</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name)</pre>
+                      <pre class="language-r">                            adtte_vars = list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">44</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
+                      <pre class="language-r">                              aval = "AVAL",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">45</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_summary_funs(summary_funs, null.ok = TRUE)</pre>
+                      <pre class="language-r">                              is_event = "is_event",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">46</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">                              paramcd = "PARAMCD",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">47</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
+                      <pre class="language-r">                              usubjid = "USUBJID",</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                              avalu = "AVALU"</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">49</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal::module(</pre>
+                      <pre class="language-r">                            ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">50</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label,</pre>
+                      <pre class="language-r">                            exclude_assays = "counts",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">51</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server = srv_g_boxplot,</pre>
+                      <pre class="language-r">                            summary_funs = list(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">52</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    server_args = list(</pre>
+                      <pre class="language-r">                              Mean = colMeans,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">53</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">                              Median = matrixStats::colMedians,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">54</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">                              Max = matrixStats::colMaxs</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">55</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">                            ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">                            pre_output = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">57</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui = ui_g_boxplot,</pre>
+                      <pre class="language-r">                            post_output = NULL,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">58</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ui_args = list(</pre>
+                      <pre class="language-r">                            plot_height = c(600L, 200L, 2000L),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">59</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name,</pre>
+                      <pre class="language-r">                            plot_width = c(1360L, 500L, 2000L)) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">60</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      summary_funs = summary_funs,</pre>
+                      <pre class="language-r">  logger::log_info("Initializing tm_g_forest_tte")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">61</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      pre_output = pre_output,</pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">62</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      post_output = post_output</pre>
+                      <pre class="language-r">  assert_string(adtte_name)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">63</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">64</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    datanames = mae_name</pre>
+                      <pre class="language-r">  assert_adtte_vars(adtte_vars)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">65</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">66</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  assert_summary_funs(summary_funs)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">67</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">68</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_boxplot sets up the user interface.</pre>
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">70</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">71</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">ui_g_boxplot &lt;- function(id,</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">72</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         data,</pre>
+                      <pre class="language-r">    server = srv_g_forest_tte,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">73</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         mae_name,</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">74</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         summary_funs,</pre>
+                      <pre class="language-r">      adtte_name = adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">75</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         pre_output,</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">76</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                         post_output) {</pre>
+                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">77</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(id)</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">78</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">79</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    encoding = div(</pre>
+                      <pre class="language-r">      plot_height = plot_height,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">80</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ### Reporter</pre>
+                      <pre class="language-r">      plot_width = plot_width</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">81</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">82</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ###</pre>
+                      <pre class="language-r">    ui = ui_g_forest_tte,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">83</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">84</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
+                      <pre class="language-r">      adtte_name = adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">85</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">86</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">87</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      geneSpecInput(ns("genes"), summary_funs),</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">88</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Jitter"),</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">89</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      shinyWidgets::switchInput(ns("jitter"), value = FALSE, size = "mini"),</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="missed">
                     <td class="num">90</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tags$label("Violin Plot"),</pre>
+                      <pre class="language-r">    datanames = c(adtte_name, mae_name)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">91</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      shinyWidgets::switchInput(ns("violin"), value = FALSE, size = "mini"),</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">92</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.widgets::panel_group(</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">93</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        teal.widgets::panel_item(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">94</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input_id = "settings_item",</pre>
+                      <pre class="language-r">#' @describeIn tm_g_forest_tte sets up the user interface.</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">95</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          collapsed = TRUE,</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">96</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          title = "Additional Settings",</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">97</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("strat"), "Optional stratifying variable"),</pre>
+                      <pre class="language-r">ui_g_forest_tte &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">98</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("color"), "Optional color variable"),</pre>
+                      <pre class="language-r">                            data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">99</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          sampleVarSpecInput(ns("facet"), "Optional facet variable")</pre>
+                      <pre class="language-r">                            adtte_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">                            mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">                            summary_funs,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
+                      <pre class="language-r">                            pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
+                  <tr class="never">
                     <td class="num">103</td>
-                    <td class="coverage">1<em>x</em></td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
+                      <pre class="language-r">                            post_output) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">104</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pre_output = pre_output,</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
                     <td class="num">105</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    post_output = post_output</pre>
+                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">106</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">    encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      ### Reporter</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">108</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_boxplot sets up the server with reactive graph.</pre>
+                      <pre class="language-r">      ###</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">110</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">111</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">112</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">srv_g_boxplot &lt;- function(id,</pre>
+                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">113</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          data,</pre>
+                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">114</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          filter_panel_api,</pre>
+                      <pre class="language-r">      geneSpecInput(ns("genes"), summary_funs),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">115</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          reporter,</pre>
+                      <pre class="language-r">      helpText("Analysis of ADTTE:", tags$code(adtte_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">116</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          mae_name,</pre>
+                      <pre class="language-r">      adtteSpecInput(ns("adtte")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">117</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          exclude_assays,</pre>
+                      <pre class="language-r">      teal.widgets::panel_group(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">118</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                          summary_funs) {</pre>
+                      <pre class="language-r">        teal.widgets::panel_item(</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">119</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
+                      <pre class="language-r">          input_id = "settings_item",</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">120</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
+                      <pre class="language-r">          collapsed = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">121</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">          title = "Additional Settings",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">122</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          sliderInput(ns("probs"), label = ("Probability Cutoff"), min = 0.01, max = 0.99, value = 0.5),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">123</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("subgroups"), "Select Categorical Subgroup Variable")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">124</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">125</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "experiment",</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">126</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data,</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">127</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="covered">
                     <td class="num">128</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae_name = mae_name</pre>
+                      <pre class="language-r">    pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="covered">
                     <td class="num">129</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    post_output = post_output</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">130</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">131</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "assay",</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">132</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = experiment$assays,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">133</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
+                      <pre class="language-r">#' @describeIn tm_g_forest_tte sets up the server with reactive graph.</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">135</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    multi &lt;- multiSampleVarSpecServer(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">136</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      inputIds = c("strat", "color", "facet"),</pre>
+                      <pre class="language-r">srv_g_forest_tte &lt;- function(id,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">137</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_name = experiment$name,</pre>
+                      <pre class="language-r">                             data,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">138</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      original_data = experiment$data</pre>
+                      <pre class="language-r">                             filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                             reporter,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">140</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    genes &lt;- geneSpecServer(</pre>
+                      <pre class="language-r">                             adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">141</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      "genes",</pre>
+                      <pre class="language-r">                             mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">142</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      funs = summary_funs,</pre>
+                      <pre class="language-r">                             adtte_vars,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">143</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      gene_choices = experiment$genes</pre>
+                      <pre class="language-r">                             exclude_assays,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">                             summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">145</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    plot_r &lt;- reactive({</pre>
+                      <pre class="language-r">                             plot_height,</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      # Resolve all reactivity.</pre>
+                      <pre class="language-r">                             plot_width) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">147</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      experiment_data &lt;- multi$experiment_data()</pre>
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">148</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      strat &lt;- multi$vars$strat()</pre>
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">149</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes &lt;- genes()</pre>
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">150</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      facet &lt;- multi$vars$facet()</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">151</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      color &lt;- multi$vars$color()</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">152</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assay &lt;- assay()</pre>
+                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">153</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      jitter &lt;- input$jitter</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">154</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      violin &lt;- input$violin</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">155</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">156</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(</pre>
+                      <pre class="language-r">      mae_name = mae_name</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">157</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">158</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        # Note: The following statements are important to make sure the UI inputs have been updated.</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">159</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        isTRUE(assay %in% SummarizedExperiment::assayNames(experiment_data)),</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">160</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is.null(facet) || isTRUE(facet %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                      <pre class="language-r">      assays = experiment$assays,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">161</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is.null(color) || isTRUE(color %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">162</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        is.null(strat) || isTRUE(strat %in% names(SummarizedExperiment::colData(experiment_data))),</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">163</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        cancelOutput = FALSE</pre>
+                      <pre class="language-r">    genes &lt;- geneSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">164</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">      "genes",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">165</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      funs = summary_funs,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">166</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate_gene_spec(genes, rownames(experiment_data))</pre>
+                      <pre class="language-r">      gene_choices = experiment$genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">167</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">168</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      hermes::draw_boxplot(</pre>
+                      <pre class="language-r">    subgroups &lt;- sampleVarSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">169</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        object = experiment_data,</pre>
+                      <pre class="language-r">      "subgroups",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">170</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assay_name = assay,</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">171</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        genes = genes,</pre>
+                      <pre class="language-r">      original_data = experiment$data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">172</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        x_var = strat,</pre>
+                      <pre class="language-r">      categorical_only = TRUE,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">173</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        facet_var = facet,</pre>
+                      <pre class="language-r">      explicit_na = TRUE</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">174</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        color_var = color,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">175</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        jitter = jitter,</pre>
+                      <pre class="language-r">    adtte &lt;- adtteSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">176</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        violin = violin</pre>
+                      <pre class="language-r">      "adtte",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">177</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">178</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">      adtte_name = adtte_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">179</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    output$plot &lt;- renderPlot(plot_r())</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">180</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">181</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
+                      <pre class="language-r">      experiment_data = subgroups$experiment_data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">182</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      id = "plot",</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">183</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      plot_r = plot_r</pre>
+                      <pre class="language-r">      assay = assay,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">184</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">      genes = genes,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">185</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      probs = reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">186</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ### REPORTER</pre>
+                      <pre class="language-r">        input$probs</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">187</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    if (with_reporter) {</pre>
+                      <pre class="language-r">      })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">188</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      card_fun &lt;- function(comment) {</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">189</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card &lt;- teal::TealReportCard$new()</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">190</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$set_name("Boxplot")</pre>
+                      <pre class="language-r">    surv_subgroups &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">191</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Boxplot", "header2")</pre>
+                      <pre class="language-r">      binned_adtte &lt;- adtte$binned_adtte_subset()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">192</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_fs(filter_panel_api$get_filter_state())</pre>
+                      <pre class="language-r">      subgroups_var &lt;- subgroups$sample_var()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">193</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">194</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                      <pre class="language-r">      tern::extract_survival_subgroups(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">195</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Experiment:",</pre>
+                      <pre class="language-r">        variables = list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">196</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`experiment-name`,</pre>
+                      <pre class="language-r">          tte = adtte_vars$aval,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">197</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nAssay:",</pre>
+                      <pre class="language-r">          is_event = adtte_vars$is_event,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">198</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`assay-name`,</pre>
+                      <pre class="language-r">          arm = adtte$gene_factor,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">199</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nFacetting Variable:",</pre>
+                      <pre class="language-r">          subgroups = subgroups_var</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">200</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`facet-sample_var`,</pre>
+                      <pre class="language-r">        ),</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">201</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nGenes Selected:",</pre>
+                      <pre class="language-r">        label_all = "All Patients",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">202</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste0(genes()$get_gene_labels(), collapse = ", "),</pre>
+                      <pre class="language-r">        data = binned_adtte</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">203</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nGene Summary:",</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">204</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`genes-fun_name`,</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">205</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nJitter:",</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">206</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$jitter,</pre>
+                      <pre class="language-r">    result &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">207</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nViolin:",</pre>
+                      <pre class="language-r">      surv_subgroups &lt;- surv_subgroups()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">208</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$violin,</pre>
+                      <pre class="language-r">      lyt &lt;- rtables::basic_table()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">209</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nOptional Stratifying Variable:",</pre>
+                      <pre class="language-r">      time_unit &lt;- adtte$time_unit()</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">210</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`strat-sample_var`,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">211</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nOptional Color Variable:",</pre>
+                      <pre class="language-r">      tern::tabulate_survival_subgroups(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">212</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`color-sample_var`,</pre>
+                      <pre class="language-r">        lyt = lyt,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">213</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "\nOptional Facet Variable:",</pre>
+                      <pre class="language-r">        df = surv_subgroups,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">214</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          input$`facet-sample_var`</pre>
+                      <pre class="language-r">        vars = c("n_tot_events", "n", "n_events", "median", "hr", "ci"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">215</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        )</pre>
+                      <pre class="language-r">        time_unit = time_unit</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">216</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">217</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">218</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">219</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
+                      <pre class="language-r">    forest_plot &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">220</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        } else {</pre>
+                      <pre class="language-r">      result &lt;- result()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">221</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
+                      <pre class="language-r">      tern::g_forest(result)</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">222</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
@@ -27800,4865 +27904,4873 @@ <h2>teal.modules.hermes coverage - 26.54%</h2>
                     <td class="num">224</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
+                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">225</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
+                      <pre class="language-r">      id = "plot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">226</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card$append_plot(plot_r(), dim = pws$dim())</pre>
+                      <pre class="language-r">      plot_r = forest_plot,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">227</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        if (!comment == "") {</pre>
+                      <pre class="language-r">      height = plot_height,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">228</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
+                      <pre class="language-r">      width = plot_width</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">229</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          card$append_text(comment)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">230</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
+                  <tr class="never">
                     <td class="num">231</td>
-                    <td class="coverage">!</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        card</pre>
+                      <pre class="language-r">    ### REPORTER</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">232</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
                     <td class="num">233</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">234</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    }</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">235</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ###</pre>
+                      <pre class="language-r">          title = "Forest Plot",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">236</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">237</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">238</td>
-                    <td class="coverage"></td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
                     </td>
                   </tr>
                   <tr class="never">
                     <td class="num">239</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @describeIn tm_g_boxplot sample module function.</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
+                  <tr class="missed">
                     <td class="num">240</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">241</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        encodings_list &lt;- list(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">242</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "Experiment:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">243</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          input$`experiment-name`,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">244</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "\nAssay:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">245</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          input$`assay-name`,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">246</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "\nGenes Selected:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">247</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          paste0(genes()$get_gene_labels(), collapse = ", "),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">248</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "\nGene Summary:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">249</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          input$`genes-fun_name`,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">250</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "\nEndpoint:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">251</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          input$`adtte-paramcd`,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">252</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "\nProbability Cutoff:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">253</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          input$probs,</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">254</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          "\nSubgroup Variable:",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">255</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">          input$`subgroups-sample_var`</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">256</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">        )</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">257</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">241</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">258</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">242</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">259</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">243</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">260</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
+                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">244</td>
+                    <td class="num">261</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">245</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">262</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   sample_tm_g_boxplot()</pre>
+                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">246</td>
+                    <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">247</td>
+                    <td class="num">264</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">sample_tm_g_boxplot &lt;- function() {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">248</td>
+                    <td class="num">265</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">249</td>
+                    <td class="num">266</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae_data &lt;- teal.data::dataset("MAE", mae)</pre>
+                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">250</td>
+                    <td class="num">267</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data &lt;- teal.data::teal_data(mae_data)</pre>
+                      <pre class="language-r">        card$append_plot(forest_plot(), dim = pws$dim())</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">251</td>
+                    <td class="num">268</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  app &lt;- teal::init(</pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">252</td>
+                    <td class="num">269</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data = data,</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">253</td>
+                    <td class="num">270</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    modules = teal::modules(</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">254</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">271</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      tm_g_boxplot(</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">255</td>
+                    <td class="num">272</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        label = "boxplot",</pre>
+                      <pre class="language-r">        card</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">273</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">256</td>
+                    <td class="num">274</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        mae_name = "MAE"</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">257</td>
+                    <td class="num">275</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">258</td>
+                    <td class="num">276</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">259</td>
+                    <td class="num">277</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">260</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">278</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">261</td>
+                    <td class="num">279</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/experimentSpec.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">280</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Input for Experiment Specification</pre>
+                      <pre class="language-r">#' @describeIn tm_g_forest_tte sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">281</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">282</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">283</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">284</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the input for the experiment specification.</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">285</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">286</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'   sample_tm_g_forest_tte()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">287</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_experiments (`string`)\cr label for the experiment selection.</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">288</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">sample_tm_g_forest_tte &lt;- function() { # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">289</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The UI part.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">290</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [experimentSpecServer()] for the module server and a complete example.</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">291</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">  adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">292</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">experimentSpecInput &lt;- function(inputId, # nolint</pre>
+                      <pre class="language-r">    dplyr::mutate(is_event = .data$CNSR == 0)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">293</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                data,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">294</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                mae_name,</pre>
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">295</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                label_experiments = "Select Experiment") {</pre>
+                      <pre class="language-r">    teal.data::dataset(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">17</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">296</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(inputId)</pre>
+                      <pre class="language-r">      "ADTTE",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">18</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">297</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name, min.chars = 1L)</pre>
+                      <pre class="language-r">      adtte,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">19</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">298</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_experiments, min.chars = 1L)</pre>
+                      <pre class="language-r">      code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">20</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">299</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  mae &lt;- data[[mae_name]]()</pre>
+                      <pre class="language-r">        dplyr::mutate(is_event = .data$CNSR == 0)"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">21</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">300</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    ),</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">301</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    teal.data::dataset("MAE", mae)</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">302</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  name_choices &lt;- names(mae)</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">303</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">23</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">304</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">24</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">305</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  selectInput(</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">25</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">306</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    inputId = ns("name"),</pre>
+                      <pre class="language-r">    modules = teal::modules(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">26</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">307</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    label = label_experiments,</pre>
+                      <pre class="language-r">      tm_g_forest_tte(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">27</td>
-                    <td class="coverage">9<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">308</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    choices = name_choices</pre>
+                      <pre class="language-r">        label = "forest",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">28</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">309</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">        adtte_name = "ADTTE",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">29</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">310</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">        mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">311</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">312</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function to Order Gene Choices</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">313</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">33</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">314</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">  shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">315</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/assaySpec.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' The possible gene choices are ordered as follows. First come all genes which</pre>
+                      <pre class="language-r">#' Module Input for Assay Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' have a non-empty name, ordered by their name alphabetically. Last come</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' all genes with an empty name, ordered by their ID alphabetically.</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param genes (`data.frame`)\cr containing `id` and `name` columns of the</pre>
+                      <pre class="language-r">#' This defines the input for the assay specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">40</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   gene choices. Note that no missing values are allowed.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">41</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The ordered `data.frame`.</pre>
+                      <pre class="language-r">#' @param label_assays (`string`)\cr label for the assay selection.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @return The UI part.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#' @seealso [assaySpecServer()] for the module server and a complete example.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' genes &lt;- data.frame(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   id = c("7", "1", "2", "345346", "0"),</pre>
+                      <pre class="language-r">assaySpecInput &lt;- function(inputId, # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   name = c("e", "", "c", "", "a")</pre>
+                      <pre class="language-r">                           label_assays = "Select Assay") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">49</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">15</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' )</pre>
+                      <pre class="language-r">  assert_string(inputId)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">50</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">16</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' h_order_genes(genes)</pre>
+                      <pre class="language-r">  assert_string(label_assays, min.chars = 1L)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_order_genes &lt;- function(genes) {</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">52</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">18</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_data_frame(genes, types = "character", any.missing = FALSE)</pre>
+                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">53</td>
-                    <td class="coverage">4<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_set_equal(names(genes), c("id", "name"))</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">54</td>
-                    <td class="coverage"></td>
+                    <td class="num">19</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  tagList(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">20</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  has_empty_name &lt;- genes$name == ""</pre>
+                      <pre class="language-r">    selectizeInput(</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">56</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">21</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  first_genes &lt;- which(!has_empty_name)[order(genes[!has_empty_name, ]$name)]</pre>
+                      <pre class="language-r">      inputId = ns("name"),</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">57</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">22</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  last_genes &lt;- which(has_empty_name)[order(genes[has_empty_name, ]$id)]</pre>
+                      <pre class="language-r">      label = label_assays,</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">58</td>
-                    <td class="coverage">4<em>x</em></td>
+                    <td class="num">23</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  genes[c(first_genes, last_genes), ]</pre>
+                      <pre class="language-r">      choices = character(0),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">59</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">24</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      options = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">60</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">25</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">        placeholder = "- Nothing selected -"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function to Format Gene Choices</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">63</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">28</td>
+                    <td class="coverage">9<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">    include_js_files("dropdown.js")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Given a [`hermes::AnyHermesData`] data object, as well as the annotation</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' column name to use as gene name, this function formats the contained genes</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' as a `data.frame` ready for consumption in [h_order_genes()] e.g.</pre>
+                      <pre class="language-r">#' Module Server for Assay Specification</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @details</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Note that missing names or names that only contain whitespace</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' are replaced by empty strings for consistency and better labeling in the</pre>
+                      <pre class="language-r">#' This defines the server part for the assay specification.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' UI downstream</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams function_arguments</pre>
+                      <pre class="language-r">#' @param assays (reactive `character`)\cr available assays in the currently selected experiment.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams experimentSpecServer</pre>
+                      <pre class="language-r">#' @return The chosen assay as a reactive string.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return A `data.frame` with `id` and `name` columns containing all genes from</pre>
+                      <pre class="language-r">#' @seealso [assaySpecInput()] for the module UI.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">78</td>
+                    <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   `object`.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">80</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">82</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' object &lt;- hermes::hermes_data[1:10, ]</pre>
+                      <pre class="language-r">#' ui &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">83</td>
+                    <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' h_gene_data(object, "symbol")</pre>
+                      <pre class="language-r">#'                data) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">84</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_gene_data &lt;- function(object, name_annotation) {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">85</td>
-                    <td class="coverage">2<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_true(hermes::is_hermes_data(object))</pre>
+                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">86</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">50</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(name_annotation, null.ok = TRUE)</pre>
+                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">87</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'     encoding = div(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">88</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">52</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  gene_ids &lt;- hermes::genes(object)</pre>
+                      <pre class="language-r">#'       experimentSpecInput(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">89</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">53</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  gene_names &lt;- if (!is.null(name_annotation)) {</pre>
+                      <pre class="language-r">#'         ns("experiment"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">90</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">54</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    annotation_data &lt;- hermes::annotation(object)</pre>
+                      <pre class="language-r">#'         data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">91</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">55</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assert_subset(name_annotation, names(annotation_data))</pre>
+                      <pre class="language-r">#'         "MAE"</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">92</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">56</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    annotation_vector &lt;- annotation_data[[name_annotation]]</pre>
+                      <pre class="language-r">#'       ),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">93</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">57</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    annotation_missing &lt;- is.na(annotation_vector) | grepl("^\\s+$", annotation_vector)</pre>
+                      <pre class="language-r">#'       assaySpecInput(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">94</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">58</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    annotation_vector[annotation_missing] &lt;- ""</pre>
+                      <pre class="language-r">#'         ns("assay"),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">95</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">59</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    annotation_vector</pre>
+                      <pre class="language-r">#'         label_assays = "Please choose assay"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">96</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  } else {</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">97</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ""</pre>
+                      <pre class="language-r">#'     ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
+                      <pre class="language-r">#'     output = textOutput(ns("result"))</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">99</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">63</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  data.frame(</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">100</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    id = gene_ids,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">101</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">65</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    name = gene_names</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">102</td>
+                    <td class="num">66</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">#' server &lt;- function(id, data, filter_panel_api) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">67</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'   moduleServer(id, module = function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">68</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'     experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">69</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Server for Experiment Specification</pre>
+                      <pre class="language-r">#'       id = "experiment",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">106</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">71</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#'       filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">108</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'       mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">73</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the server part for the experiment specification.</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">110</td>
+                    <td class="num">74</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">111</td>
+                    <td class="num">75</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">#'       "assay",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">76</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param name_annotation (`string` or `NULL`)\cr which annotation column to use as name</pre>
+                      <pre class="language-r">#'       experiment$assays,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">113</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   to return in the `genes` data. If `NULL`, then the `name` column will be set to empty</pre>
+                      <pre class="language-r">#'       exclude_assays = c("counts", "cpm", "tpm", "bla")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">114</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   strings.</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">115</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param sample_vars_as_factors (`flag`)\cr whether to convert the sample variables</pre>
+                      <pre class="language-r">#'     output$result &lt;- renderPrint({</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">116</td>
+                    <td class="num">80</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   (columns in `colData()` of the experiment) from character to factor variables.</pre>
+                      <pre class="language-r">#'       assay()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">117</td>
+                    <td class="num">81</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param with_mae_col_data (`flag`)\cr whether to include the `colData()` of the</pre>
+                      <pre class="language-r">#'     })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">118</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   MAE into the experiment `colData()`.</pre>
+                      <pre class="language-r">#'   })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">119</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return List with the following reactive objects:</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">120</td>
+                    <td class="num">84</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `data`: the [`hermes::AnyHermesData`] experiment.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">121</td>
+                    <td class="num">85</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `name`: the name of the experiment as selected by the user.</pre>
+                      <pre class="language-r">#' my_app &lt;- function() {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">86</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `genes`: a `data.frame` with the genes in `data`, with columns `id` and `name`.</pre>
+                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">123</td>
+                    <td class="num">87</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   - `assays`: the names of the assays in `data`.</pre>
+                      <pre class="language-r">#'   mae_name &lt;- "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">124</td>
+                    <td class="num">88</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   mae_data &lt;- dataset(mae_name, mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">125</td>
+                    <td class="num">89</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [experimentSpecInput()] for the module UI.</pre>
+                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">90</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">127</td>
+                    <td class="num">91</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'     data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">128</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     modules = modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">129</td>
+                    <td class="num">93</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#'       module(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">130</td>
+                    <td class="num">94</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ui &lt;- function(id,</pre>
+                      <pre class="language-r">#'         label = "assaySpec example",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">131</td>
+                    <td class="num">95</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                data,</pre>
+                      <pre class="language-r">#'         server = server,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">132</td>
+                    <td class="num">96</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                mae_name) {</pre>
+                      <pre class="language-r">#'         ui = ui,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
+                      <pre class="language-r">#'         datanames = "all"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">134</td>
+                    <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">#'       )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">135</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     encoding = div(</pre>
+                      <pre class="language-r">#'     )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">136</td>
+                    <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experimentSpecInput(</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">137</td>
+                    <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ns("my_experiment"),</pre>
+                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">138</td>
+                    <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         data,</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">139</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         mae_name,</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">140</td>
+                    <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label_experiments = "Please choose experiment"</pre>
+                      <pre class="language-r">#'   my_app()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       ),</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       selectInput(</pre>
+                      <pre class="language-r">assaySpecServer &lt;- function(id, # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">143</td>
+                    <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ns("property"),</pre>
+                      <pre class="language-r">                            assays,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">144</td>
+                    <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         "Please choose property",</pre>
+                      <pre class="language-r">                            exclude_assays = character()) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">145</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">109</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         c("data", "name", "genes", "assays")</pre>
+                      <pre class="language-r">  assert_string(id)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">146</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">110</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">  assert_reactive(assays)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">147</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">111</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     ),</pre>
+                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">148</td>
+                    <td class="num">112</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output = div(</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">149</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">113</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       verbatimTextOutput(ns("summary")),</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">150</td>
+                    <td class="num">114</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       verbatimTextOutput(ns("head"))</pre>
+                      <pre class="language-r">    # When the assay names change, update the choices for assay.</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">151</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">115</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">    choices &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">152</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">116</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">      assays &lt;- assays()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">153</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">117</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">      remaining_assays &lt;- setdiff(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">154</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">118</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        assays,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">155</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">119</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' server &lt;- function(id,</pre>
+                      <pre class="language-r">        exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">156</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                    data,</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">157</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">121</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                    filter_panel_api,</pre>
+                      <pre class="language-r">      removed_assays &lt;- setdiff(assays, remaining_assays)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">158</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">122</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                    mae_name) {</pre>
+                      <pre class="language-r">      if (length(removed_assays) &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">159</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">123</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">        showNotification(type = "warning", paste(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">160</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">124</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">          "Excluded", ifelse(length(removed_assays) &gt; 1, "assays", "assay"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">161</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">125</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "my_experiment",</pre>
+                      <pre class="language-r">          hermes::h_short_list(removed_assays), "as per app specifications"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">162</td>
+                    <td class="num">126</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       data,</pre>
+                      <pre class="language-r">        ))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">163</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       filter_panel_api,</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">164</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">128</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name</pre>
+                      <pre class="language-r">      if (length(remaining_assays) == 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">165</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">129</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">        remaining_assays &lt;- character(0)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">166</td>
+                    <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     result &lt;- reactive({</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">167</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">131</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       switch(input$property,</pre>
+                      <pre class="language-r">      remaining_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">168</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         data = experiment$data(),</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">169</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         name = experiment$name(),</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">170</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">134</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         genes = experiment$genes(),</pre>
+                      <pre class="language-r">    observeEvent(choices(), {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">171</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">135</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         assays = experiment$assays()</pre>
+                      <pre class="language-r">      choices &lt;- choices()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">172</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">136</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">      updateSelectizeInput(session, "name", choices = choices)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">173</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">137</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">      session$sendCustomMessage(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">174</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">138</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output$summary &lt;- renderPrint({</pre>
+                      <pre class="language-r">        "toggle_dropdown",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">175</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">139</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       result &lt;- result()</pre>
+                      <pre class="language-r">        list(input_id = session$ns("name"), disabled = (length(choices) == 0))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">176</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       hermes::summary(result)</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">177</td>
+                    <td class="num">141</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">178</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output$head &lt;- renderPrint({</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">179</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">143</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       result &lt;- result()</pre>
+                      <pre class="language-r">    reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">180</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">144</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       utils::head(result)</pre>
+                      <pre class="language-r">      choices &lt;- choices()</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">181</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">145</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">182</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">146</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   })</pre>
+                      <pre class="language-r">        length(choices) &gt; 0,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">183</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">147</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">        "No assays eligible for this experiment, please make sure to add normalized assays"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">184</td>
+                    <td class="num">148</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">185</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">149</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' my_app &lt;- function() {</pre>
+                      <pre class="language-r">      input$name</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">186</td>
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">187</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae_name &lt;- "MAE"</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">188</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae_data &lt;- dataset(mae_name, mae)</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/checkmate.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">189</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">#' Additional Assertions for `checkmate`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">190</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   app &lt;- init(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">191</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     data = data,</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">192</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     modules = modules(</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">193</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       module(</pre>
+                      <pre class="language-r">#' We provide additional assertion functions which can be used together with</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">194</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label = "experimentSpec example",</pre>
+                      <pre class="language-r">#' the `checkmate` functions. These are described in individual help pages</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">195</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server = server,</pre>
+                      <pre class="language-r">#' linked below.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">196</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server_args = list(mae_name = mae_name),</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">197</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui = ui,</pre>
+                      <pre class="language-r">#' @return Depending on the function prefix.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">198</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui_args = list(mae_name = mae_name),</pre>
+                      <pre class="language-r">#' - `assert_` functions return the object invisibly if successful, and otherwise</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">199</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         datanames = "all"</pre>
+                      <pre class="language-r">#'   throw an error message.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">200</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">#' - `check_` functions return `TRUE` if successful, otherwise a string with the</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">201</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">#'   error message.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">202</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">#' - `test_` functions just return `TRUE` or `FALSE`.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">203</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">204</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' @seealso [assert_tag()], [assert_reactive()], [assert_summary_funs()], [assert_adtte_vars()]</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">205</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">206</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   my_app()</pre>
+                      <pre class="language-r">#' @name assertions</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">207</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">#' @import checkmate</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">208</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">experimentSpecServer &lt;- function(id, # nolint</pre>
+                      <pre class="language-r">#' @keywords internal</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">209</td>
+                    <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                 data,</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">210</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                 filter_panel_api,</pre>
+                      <pre class="language-r">NULL</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">211</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                 mae_name,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">212</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                 name_annotation = "symbol",</pre>
+                      <pre class="language-r"># assert_tag ----</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">213</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                 sample_vars_as_factors = TRUE,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">214</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                                 with_mae_col_data = TRUE) {</pre>
+                      <pre class="language-r">#' Check for Shiny Tag</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">215</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">27</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(id)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">216</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">28</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_class(data, "tdata")</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">217</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">29</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(mae_name, min.chars = 1L)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">218</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">30</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(name_annotation, min.chars = 1L, null.ok = TRUE)</pre>
+                      <pre class="language-r">#' Check whether `x` is a shiny tag.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">219</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">31</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_flag(sample_vars_as_factors)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">220</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">32</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_flag(with_mae_col_data)</pre>
+                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">221</td>
+                    <td class="num">33</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">222</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">34</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">223</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the filtered data set of the chosen experiment changes, update the</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">224</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # experiment data object.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">225</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">37</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    data_return &lt;- reactive({</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">226</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">38</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      name &lt;- input$name</pre>
+                      <pre class="language-r">#' check_tag("bla")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">227</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">39</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(name)</pre>
+                      <pre class="language-r">#' check_tag(NULL, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">228</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">40</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      mae &lt;- data[[mae_name]]()</pre>
+                      <pre class="language-r">check_tag &lt;- function(x, null.ok = FALSE) { # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">229</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">41</td>
+                    <td class="coverage">16<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      orig_object &lt;- mae[[name]]</pre>
+                      <pre class="language-r">  assert_flag(null.ok)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">230</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">42</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">  ok &lt;- (null.ok &amp;&amp; test_null(x)) || test_class(x, "shiny.tag")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">231</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">43</td>
+                    <td class="coverage">15<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        hermes::is_hermes_data(orig_object),</pre>
+                      <pre class="language-r">  if (!ok) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">232</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">44</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "Please first convert your experiment to HermesData class"</pre>
+                      <pre class="language-r">    return("Must be a 'shiny.tag' or NULL")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">233</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">  }</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">234</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">46</td>
+                    <td class="coverage">14<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">  return(TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">235</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">47</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        !hermes::isEmpty(orig_object),</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">236</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">48</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "No genes or samples included in this experiment, please adjust filters"</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">237</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">#' @rdname check_tag</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">238</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">50</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      object &lt;- if (with_mae_col_data) {</pre>
+                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">239</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">51</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        MultiAssayExperiment::getWithColData(mae, name)</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">240</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      } else {</pre>
+                      <pre class="language-r">assert_tag &lt;- makeAssertionFunction(check_tag)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">241</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">53</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        orig_object</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">242</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' @rdname check_tag</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">243</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">55</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (sample_vars_as_factors) {</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">244</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">56</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        SummarizedExperiment::colData(object) &lt;-</pre>
+                      <pre class="language-r">test_tag &lt;- makeTestFunction(check_tag)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">245</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">57</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          hermes::df_cols_to_factor(SummarizedExperiment::colData(object))</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">246</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">#' @rdname check_tag</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">247</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">59</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      object</pre>
+                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">248</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">249</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">expect_tag &lt;- makeExpectationFunction(check_tag)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">250</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the filtered data set or the chosen experiment changes, update</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">251</td>
+                    <td class="num">63</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # the calls that subset the genes of the chosen experiment data object.</pre>
+                      <pre class="language-r"># assert_reactive ----</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">252</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">64</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    subset_calls &lt;- reactive({</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">253</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">65</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      name &lt;- input$name</pre>
+                      <pre class="language-r">#' Check for Reactive Input</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">254</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">66</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      req(name)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">255</td>
+                    <td class="num">67</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">256</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">68</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_states &lt;- filter_panel_api$get_filter_state()[[mae_name]][[name]]["subset"]</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">257</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">69</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      filter_states</pre>
+                      <pre class="language-r">#' Check whether `x` is a reactive input.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">258</td>
+                    <td class="num">70</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">259</td>
+                    <td class="num">71</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">260</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # Only when the chosen gene subset changes, we recompute gene choices</pre>
+                      <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">261</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">73</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    genes &lt;- eventReactive(subset_calls(), ignoreNULL = FALSE, {</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">262</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">74</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data_return &lt;- data_return()</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">263</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">75</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes &lt;- h_gene_data(data_return, name_annotation)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">264</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">76</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      h_order_genes(genes)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">265</td>
+                    <td class="num">77</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' check_reactive("bla")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">266</td>
+                    <td class="num">78</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' check_reactive(reactive("bla"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">267</td>
+                    <td class="num">79</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the chosen experiment changes, recompute the assay names.</pre>
+                      <pre class="language-r">check_reactive &lt;- function(x) {</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">268</td>
-                    <td class="coverage">!</td>
+                  <tr class="covered">
+                    <td class="num">80</td>
+                    <td class="coverage">6<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    assays &lt;- eventReactive(input$name, ignoreNULL = TRUE, {</pre>
+                      <pre class="language-r">  inherits(x, "reactive")</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">269</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">81</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data_return &lt;- data_return()</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">270</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">82</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      SummarizedExperiment::assayNames(data_return)</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">271</td>
+                    <td class="num">83</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">#' @rdname check_reactive</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">272</td>
+                    <td class="num">84</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">273</td>
+                    <td class="num">85</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">274</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">86</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    list(</pre>
+                      <pre class="language-r">assert_reactive &lt;- makeAssertionFunction(check_reactive)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">275</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">87</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      data = data_return,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">276</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">88</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      name = reactive({</pre>
+                      <pre class="language-r">#' @rdname check_reactive</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">277</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">89</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        input$name</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">278</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">90</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }), # nolint</pre>
+                      <pre class="language-r">test_reactive &lt;- makeTestFunction(check_reactive)</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">279</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">91</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      genes = genes,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">280</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">92</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays = assays</pre>
+                      <pre class="language-r"># assert_summary_funs ----</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">281</td>
+                    <td class="num">93</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">282</td>
+                    <td class="num">94</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">#' Check for List of Summary Functions</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">283</td>
+                    <td class="num">95</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/checkmate.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
                   <tr class="never">
-                    <td class="num">1</td>
+                    <td class="num">96</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Additional Assertions for `checkmate`</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">2</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">3</td>
+                    <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#' Check whether `x` is a list of summary functions.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">5</td>
+                    <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' We provide additional assertion functions which can be used together with</pre>
+                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' the `checkmate` functions. These are described in individual help pages</pre>
+                      <pre class="language-r">#' @param null.ok (`flag`)\cr whether `x` may also contain `NULL`, meaning that</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' linked below.</pre>
+                      <pre class="language-r">#'   a user choice is possible where no summary function should be applied.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Depending on the function prefix.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">105</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' - `assert_` functions return the object invisibly if successful, and otherwise</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   throw an error message.</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">12</td>
+                    <td class="num">107</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' - `check_` functions return `TRUE` if successful, otherwise a string with the</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">108</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   error message.</pre>
+                      <pre class="language-r">#' assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' - `test_` functions just return `TRUE` or `FALSE`.</pre>
+                      <pre class="language-r">assert_summary_funs &lt;- function(x, null.ok = FALSE) { # nolint</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">110</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_flag(null.ok)</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">111</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  assert_list(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">112</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    x,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">113</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [assert_tag()], [assert_reactive()], [assert_summary_funs()], [assert_adtte_vars()]</pre>
+                      <pre class="language-r">    types = c("function", `if`(null.ok, "null", NULL)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">17</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">114</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    min.len = 1L,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">115</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @name assertions</pre>
+                      <pre class="language-r">    unique = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">116</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @import checkmate</pre>
+                      <pre class="language-r">    names = "unique"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">20</td>
+                    <td class="num">117</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @keywords internal</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">21</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">118</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  invisible(x)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">22</td>
+                    <td class="num">119</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">NULL</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">23</td>
+                    <td class="num">120</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">24</td>
+                    <td class="num">121</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># assert_tag ----</pre>
+                      <pre class="language-r"># assert_adtte_vars ----</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">25</td>
+                    <td class="num">122</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">123</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check for Shiny Tag</pre>
+                      <pre class="language-r">#' Check for `ADTTE` Variables</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">124</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">125</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">126</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">30</td>
+                    <td class="num">127</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check whether `x` is a shiny tag.</pre>
+                      <pre class="language-r">#' Check whether `x` is a list of `ADTTE` variables.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">128</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">32</td>
+                    <td class="num">129</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @inheritParams assertion_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">33</td>
+                    <td class="num">130</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">35</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">37</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">38</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' check_tag("bla")</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">39</td>
+                    <td class="num">135</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' check_tag(NULL, null.ok = TRUE)</pre>
+                      <pre class="language-r">#' assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">40</td>
+                    <td class="num">136</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">check_tag &lt;- function(x, null.ok = FALSE) { # nolint</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">41</td>
-                    <td class="coverage">16<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_flag(null.ok)</pre>
+                      <pre class="language-r">assert_adtte_vars &lt;- function(x) {</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">42</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">137</td>
+                    <td class="coverage">3<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  ok &lt;- (null.ok &amp;&amp; test_null(x)) || test_class(x, "shiny.tag")</pre>
+                      <pre class="language-r">  assert_list(x, types = "character", names = "unique", unique = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">43</td>
-                    <td class="coverage">15<em>x</em></td>
+                    <td class="num">138</td>
+                    <td class="coverage">2<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  if (!ok) {</pre>
+                      <pre class="language-r">  assert_names(names(x), permutation.of = c("aval", "is_event", "paramcd", "usubjid", "avalu"))</pre>
                     </td>
                   </tr>
                   <tr class="covered">
-                    <td class="num">44</td>
+                    <td class="num">139</td>
                     <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    return("Must be a 'shiny.tag' or NULL")</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">45</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  }</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">46</td>
-                    <td class="coverage">14<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  return(TRUE)</pre>
+                      <pre class="language-r">  invisible(x)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>
                     </td>
                   </tr>
+                </tbody>
+              </table>
+            </div>
+            <div id="R/km.R" class="hidden">
+              <table class="table-condensed">
+                <tbody>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">1</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' Teal Module for `Kaplan-Meier` Plot</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">2</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname check_tag</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">50</td>
+                    <td class="num">3</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
+                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">4</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">5</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">assert_tag &lt;- makeAssertionFunction(check_tag)</pre>
+                      <pre class="language-r">#' This teal module produces a grid style `Kaplan-Meier` plot for data with</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">6</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' `ADaM` structure.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">7</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname check_tag</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">55</td>
+                    <td class="num">8</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">9</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">test_tag &lt;- makeTestFunction(check_tag)</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">10</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' @return Shiny module to be used in the teal app.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">11</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname check_tag</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">12</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">60</td>
+                    <td class="num">13</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">61</td>
+                    <td class="num">14</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">expect_tag &lt;- makeExpectationFunction(check_tag)</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">62</td>
+                    <td class="num">15</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">16</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># assert_reactive ----</pre>
+                      <pre class="language-r">#' adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">17</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#'   dplyr::mutate(is_event = (.data$CNSR == 0))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">18</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check for Reactive Input</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">19</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' data &lt;- teal_data(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">20</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">#'   dataset(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">21</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     "ADTTE",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">22</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check whether `x` is a reactive input.</pre>
+                      <pre class="language-r">#'     adtte,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">23</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'     code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">24</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
+                      <pre class="language-r">#'       dplyr::mutate(is_event = (.data$CNSR == 0))"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">25</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
+                      <pre class="language-r">#'   ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">26</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">27</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">28</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">29</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">#' modules &lt;- modules(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">30</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' check_reactive("bla")</pre>
+                      <pre class="language-r">#'   tm_g_km(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">78</td>
+                    <td class="num">31</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' check_reactive(reactive("bla"))</pre>
+                      <pre class="language-r">#'     label = "kaplan-meier",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">32</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">check_reactive &lt;- function(x) {</pre>
+                      <pre class="language-r">#'     adtte_name = "ADTTE",</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">80</td>
-                    <td class="coverage">6<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">33</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  inherits(x, "reactive")</pre>
+                      <pre class="language-r">#'     mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">34</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">#'   )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">82</td>
+                    <td class="num">35</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">83</td>
+                    <td class="num">36</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname check_reactive</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">84</td>
+                    <td class="num">37</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
+                      <pre class="language-r">#' app &lt;- init(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">85</td>
+                    <td class="num">38</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#'   data = data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">86</td>
+                    <td class="num">39</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">assert_reactive &lt;- makeAssertionFunction(check_reactive)</pre>
+                      <pre class="language-r">#'   modules = modules</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">87</td>
+                    <td class="num">40</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">88</td>
+                    <td class="num">41</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @rdname check_reactive</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">89</td>
+                    <td class="num">42</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">90</td>
+                    <td class="num">43</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">test_reactive &lt;- makeTestFunction(check_reactive)</pre>
+                      <pre class="language-r">#'   shinyApp(ui = app$ui, server = app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">91</td>
+                    <td class="num">44</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">92</td>
+                    <td class="num">45</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># assert_summary_funs ----</pre>
+                      <pre class="language-r">tm_g_km &lt;- function(label,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">93</td>
+                    <td class="num">46</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">                    adtte_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">94</td>
+                    <td class="num">47</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check for List of Summary Functions</pre>
+                      <pre class="language-r">                    mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">95</td>
+                    <td class="num">48</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                    adtte_vars = list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">96</td>
+                    <td class="num">49</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">                      aval = "AVAL",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">97</td>
+                    <td class="num">50</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                      is_event = "is_event",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">98</td>
+                    <td class="num">51</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check whether `x` is a list of summary functions.</pre>
+                      <pre class="language-r">                      paramcd = "PARAMCD",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">52</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                      usubjid = "USUBJID",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">100</td>
+                    <td class="num">53</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
+                      <pre class="language-r">                      avalu = "AVALU"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">101</td>
+                    <td class="num">54</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param null.ok (`flag`)\cr whether `x` may also contain `NULL`, meaning that</pre>
+                      <pre class="language-r">                    ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">102</td>
+                    <td class="num">55</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   a user choice is possible where no summary function should be applied.</pre>
+                      <pre class="language-r">                    exclude_assays = "counts",</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">103</td>
+                    <td class="num">56</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
+                      <pre class="language-r">                    summary_funs = list(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">57</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                      Mean = colMeans,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">105</td>
+                    <td class="num">58</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">                      Median = matrixStats::colMedians,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">106</td>
+                    <td class="num">59</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">                      Max = matrixStats::colMaxs</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">60</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">                    ),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">108</td>
+                    <td class="num">61</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)</pre>
+                      <pre class="language-r">                    pre_output = NULL,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">109</td>
+                    <td class="num">62</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">assert_summary_funs &lt;- function(x, null.ok = FALSE) { # nolint</pre>
+                      <pre class="language-r">                    post_output = NULL) {</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">110</td>
+                    <td class="num">63</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_flag(null.ok)</pre>
+                      <pre class="language-r">  logger::log_info("Initializing tm_g_km")</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">111</td>
+                    <td class="num">64</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_list(</pre>
+                      <pre class="language-r">  assert_string(label)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">112</td>
+                    <td class="num">65</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x,</pre>
+                      <pre class="language-r">  assert_string(adtte_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">113</td>
+                    <td class="num">66</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    types = c("function", `if`(null.ok, "null", NULL)),</pre>
+                      <pre class="language-r">  assert_string(mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">114</td>
+                    <td class="num">67</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    min.len = 1L,</pre>
+                      <pre class="language-r">  assert_adtte_vars(adtte_vars)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">115</td>
+                    <td class="num">68</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    unique = TRUE,</pre>
+                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">116</td>
+                    <td class="num">69</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    names = "unique"</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">117</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">  assert_summary_funs(summary_funs)</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">118</td>
+                    <td class="num">70</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  invisible(x)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">119</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">120</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">  assert_tag(pre_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">121</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">71</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"># assert_adtte_vars ----</pre>
+                      <pre class="language-r">  assert_tag(post_output, null.ok = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">122</td>
+                    <td class="num">72</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">123</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' Check for `ADTTE` Variables</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">124</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">125</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">126</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">127</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">73</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Check whether `x` is a list of `ADTTE` variables.</pre>
+                      <pre class="language-r">  teal::module(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">128</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">74</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">129</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">75</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams assertion_arguments</pre>
+                      <pre class="language-r">    server = srv_g_km,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">130</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">76</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [`assertions`] for more details.</pre>
+                      <pre class="language-r">    server_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">131</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">77</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      adtte_name = adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">132</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">78</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">133</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">79</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">134</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">80</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">135</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">81</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' assert_adtte_vars(list(aval = "AV", is_event = "EV", paramcd = "PC", usubjid = "ID", avalu = "u"))</pre>
+                      <pre class="language-r">      summary_funs = summary_funs</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">136</td>
+                    <td class="num">82</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">assert_adtte_vars &lt;- function(x) {</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">137</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">83</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_list(x, types = "character", names = "unique", unique = TRUE)</pre>
+                      <pre class="language-r">    ui = ui_g_km,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">138</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">84</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_names(names(x), permutation.of = c("aval", "is_event", "paramcd", "usubjid", "avalu"))</pre>
+                      <pre class="language-r">    ui_args = list(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">139</td>
-                    <td class="coverage">1<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">85</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  invisible(x)</pre>
+                      <pre class="language-r">      adtte_name = adtte_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">140</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">86</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/assaySpec.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">87</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Input for Assay Specification</pre>
+                      <pre class="language-r">      summary_funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">88</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">89</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">      post_output = post_output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">90</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">91</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the input for the assay specification.</pre>
+                      <pre class="language-r">    datanames = c(adtte_name, mae_name)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">6</td>
+                    <td class="num">92</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">7</td>
+                    <td class="num">93</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">8</td>
+                    <td class="num">94</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param label_assays (`string`)\cr label for the assay selection.</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">9</td>
+                    <td class="num">95</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @describeIn tm_g_km sets up the user interface.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">10</td>
+                    <td class="num">96</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The UI part.</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">11</td>
+                    <td class="num">97</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [assaySpecServer()] for the module server and a complete example.</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">12</td>
+                    <td class="num">98</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">ui_g_km &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">13</td>
+                    <td class="num">99</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">assaySpecInput &lt;- function(inputId, # nolint</pre>
+                      <pre class="language-r">                    data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">14</td>
+                    <td class="num">100</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                           label_assays = "Select Assay") {</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">15</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(inputId)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">16</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(label_assays, min.chars = 1L)</pre>
+                      <pre class="language-r">                    adtte_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">17</td>
+                    <td class="num">101</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">18</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  ns &lt;- NS(inputId)</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">19</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">  tagList(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">20</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    selectizeInput(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">21</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      inputId = ns("name"),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">22</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      label = label_assays,</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">23</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      choices = character(0),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">24</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      options = list(</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">25</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">        placeholder = "- Nothing selected -"</pre>
+                      <pre class="language-r">                    mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">102</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">                    summary_funs,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">27</td>
+                    <td class="num">103</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    ),</pre>
-                    </td>
-                  </tr>
-                  <tr class="covered">
-                    <td class="num">28</td>
-                    <td class="coverage">9<em>x</em></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    include_js_files("dropdown.js")</pre>
+                      <pre class="language-r">                    pre_output,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">104</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r">                    post_output) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">30</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">105</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  ns &lt;- NS(id)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">31</td>
+                    <td class="num">106</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">32</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">107</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Module Server for Assay Specification</pre>
+                      <pre class="language-r">  teal.widgets::standard_layout(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">33</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">108</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    encoding = div(</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">34</td>
+                    <td class="num">109</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">      ### Reporter</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">110</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_ui(ns("simple_reporter")),</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">111</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This defines the server part for the assay specification.</pre>
+                      <pre class="language-r">      ###</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">37</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">112</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      tags$label("Encodings", class = "text-primary"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">38</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">113</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @inheritParams module_arguments</pre>
+                      <pre class="language-r">      helpText("Analysis of MAE:", tags$code(mae_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">39</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">114</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param assays (reactive `character`)\cr available assays in the currently selected experiment.</pre>
+                      <pre class="language-r">      experimentSpecInput(ns("experiment"), data, mae_name),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">40</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">115</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return The chosen assay as a reactive string.</pre>
+                      <pre class="language-r">      assaySpecInput(ns("assay")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">41</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">116</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      geneSpecInput(ns("genes"), summary_funs),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">42</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">117</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @seealso [assaySpecInput()] for the module UI.</pre>
+                      <pre class="language-r">      helpText("Analysis of ADTTE:", tags$code(adtte_name)),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">43</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">118</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      adtteSpecInput(ns("adtte")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">44</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">119</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">      teal.widgets::panel_group(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">45</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">120</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        teal.widgets::panel_item(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">46</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">121</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">          input_id = "settings_item",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">47</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">122</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' ui &lt;- function(id,</pre>
+                      <pre class="language-r">          collapsed = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">48</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">123</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'                data) {</pre>
+                      <pre class="language-r">          title = "Additional Settings",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">49</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">124</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   ns &lt;- NS(id)</pre>
+                      <pre class="language-r">          sampleVarSpecInput(ns("strata"), "Select Strata"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">50</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">125</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   teal.widgets::standard_layout(</pre>
+                      <pre class="language-r">          sliderInput(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">51</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">126</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     encoding = div(</pre>
+                      <pre class="language-r">            ns("percentiles"),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">52</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">127</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experimentSpecInput(</pre>
+                      <pre class="language-r">            "Select quantiles to be displayed",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">53</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">128</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ns("experiment"),</pre>
+                      <pre class="language-r">            min = 0,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">54</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">129</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         data,</pre>
+                      <pre class="language-r">            max = 1,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">55</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">130</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         "MAE"</pre>
+                      <pre class="language-r">            value = c(0, 0.5)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">56</td>
+                    <td class="num">131</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       ),</pre>
+                      <pre class="language-r">          )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">57</td>
+                    <td class="num">132</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       assaySpecInput(</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">133</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ns("assay"),</pre>
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">59</td>
+                    <td class="num">134</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label_assays = "Please choose assay"</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">60</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">135</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">    output = teal.widgets::plot_with_settings_ui(ns("plot")),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">61</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">136</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     ),</pre>
+                      <pre class="language-r">    pre_output = pre_output,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">62</td>
-                    <td class="coverage"></td>
+                  <tr class="covered">
+                    <td class="num">137</td>
+                    <td class="coverage">1<em>x</em></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output = textOutput(ns("result"))</pre>
+                      <pre class="language-r">    post_output = post_output</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">63</td>
+                    <td class="num">138</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">64</td>
+                    <td class="num">139</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">140</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">66</td>
+                    <td class="num">141</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' server &lt;- function(id, data, filter_panel_api) {</pre>
+                      <pre class="language-r">#' @describeIn tm_g_km sets up the user interface.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">142</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   moduleServer(id, module = function(input, output, session) {</pre>
+                      <pre class="language-r">#' @inheritParams module_arguments</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">143</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     experiment &lt;- experimentSpecServer(</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">69</td>
+                    <td class="num">144</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       id = "experiment",</pre>
+                      <pre class="language-r">srv_g_km &lt;- function(id,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">70</td>
+                    <td class="num">145</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       data = data,</pre>
+                      <pre class="language-r">                     data,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">146</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       filter_panel_api = filter_panel_api,</pre>
+                      <pre class="language-r">                     filter_panel_api,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">147</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       mae_name = "MAE"</pre>
+                      <pre class="language-r">                     reporter,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">148</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">                     adtte_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">74</td>
+                    <td class="num">149</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     assay &lt;- assaySpecServer(</pre>
+                      <pre class="language-r">                     mae_name,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">75</td>
+                    <td class="num">150</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       "assay",</pre>
+                      <pre class="language-r">                     adtte_vars,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">76</td>
+                    <td class="num">151</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       experiment$assays,</pre>
+                      <pre class="language-r">                     summary_funs,</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">152</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       exclude_assays = c("counts", "cpm", "tpm", "bla")</pre>
+                      <pre class="language-r">                     exclude_assays) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">78</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">153</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">  with_reporter &lt;- !missing(reporter) &amp;&amp; inherits(reporter, "Reporter")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">79</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">154</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     output$result &lt;- renderPrint({</pre>
+                      <pre class="language-r">  assert_class(filter_panel_api, "FilterPanelAPI")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">80</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">155</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       assay()</pre>
+                      <pre class="language-r">  assert_class(data, "tdata")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">81</td>
+                    <td class="num">156</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     })</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">82</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">157</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   })</pre>
+                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">83</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">158</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">    experiment &lt;- experimentSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">84</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">159</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      "experiment",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">85</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">160</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' my_app &lt;- function() {</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">86</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">161</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae &lt;- hermes::multi_assay_experiment</pre>
+                      <pre class="language-r">      filter_panel_api = filter_panel_api,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">87</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">162</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae_name &lt;- "MAE"</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">88</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">163</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   mae_data &lt;- dataset(mae_name, mae)</pre>
+                      <pre class="language-r">      sample_vars_as_factors = FALSE # To avoid converting logical `event` to factor.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">89</td>
+                    <td class="num">164</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   data &lt;- teal_data(mae_data)</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">90</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">165</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   app &lt;- init(</pre>
+                      <pre class="language-r">    assay &lt;- assaySpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">91</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">166</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     data = data,</pre>
+                      <pre class="language-r">      "assay",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">92</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">167</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     modules = modules(</pre>
+                      <pre class="language-r">      assays = experiment$assays,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">93</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">168</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       module(</pre>
+                      <pre class="language-r">      exclude_assays = exclude_assays</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">94</td>
+                    <td class="num">169</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         label = "assaySpec example",</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">95</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">170</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         server = server,</pre>
+                      <pre class="language-r">    genes &lt;- geneSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">96</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">171</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         ui = ui,</pre>
+                      <pre class="language-r">      "genes",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">97</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">172</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'         datanames = "all"</pre>
+                      <pre class="language-r">      funs = summary_funs,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">98</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">173</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'       )</pre>
+                      <pre class="language-r">      gene_choices = experiment$genes</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">99</td>
+                    <td class="num">174</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'     )</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">100</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">175</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   )</pre>
+                      <pre class="language-r">    strata &lt;- sampleVarSpecServer(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">101</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">176</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   shinyApp(app$ui, app$server)</pre>
+                      <pre class="language-r">      "strata",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">102</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">177</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">103</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">178</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' if (interactive()) {</pre>
+                      <pre class="language-r">      original_data = experiment$data</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">104</td>
+                    <td class="num">179</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'   my_app()</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">105</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">180</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' }</pre>
+                      <pre class="language-r">    percentiles_without_borders &lt;- reactive({</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">106</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">181</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">assaySpecServer &lt;- function(id, # nolint</pre>
+                      <pre class="language-r">      percentiles &lt;- input$percentiles</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">107</td>
+                    <td class="num">182</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            assays,</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">108</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">183</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">                            exclude_assays = character()) {</pre>
+                      <pre class="language-r">      result &lt;- setdiff(percentiles, c(0, 1))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">109</td>
+                    <td class="num">184</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(id)</pre>
+                      <pre class="language-r">      validate(need(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">110</td>
+                    <td class="num">185</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_reactive(assays)</pre>
+                      <pre class="language-r">        length(result) &gt; 0,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">111</td>
+                    <td class="num">186</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_character(exclude_assays, any.missing = FALSE)</pre>
+                      <pre class="language-r">        "Please select at least one quantile other than 0 and 1"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">112</td>
+                    <td class="num">187</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      ))</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">113</td>
+                    <td class="num">188</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  moduleServer(id, function(input, output, session) {</pre>
+                      <pre class="language-r">      result</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">114</td>
+                    <td class="num">189</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    # When the assay names change, update the choices for assay.</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">115</td>
+                    <td class="num">190</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    choices &lt;- reactive({</pre>
+                      <pre class="language-r">    adtte &lt;- adtteSpecServer(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">116</td>
+                    <td class="num">191</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      assays &lt;- assays()</pre>
+                      <pre class="language-r">      "adtte",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">117</td>
+                    <td class="num">192</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      remaining_assays &lt;- setdiff(</pre>
+                      <pre class="language-r">      data = data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">118</td>
+                    <td class="num">193</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        assays,</pre>
+                      <pre class="language-r">      adtte_name = adtte_name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">119</td>
+                    <td class="num">194</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        exclude_assays</pre>
+                      <pre class="language-r">      mae_name = mae_name,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">120</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">195</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">      adtte_vars = adtte_vars,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">121</td>
+                    <td class="num">196</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      removed_assays &lt;- setdiff(assays, remaining_assays)</pre>
+                      <pre class="language-r">      experiment_data = strata$experiment_data,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">122</td>
+                    <td class="num">197</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (length(removed_assays) &gt; 0) {</pre>
+                      <pre class="language-r">      experiment_name = experiment$name,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">123</td>
+                    <td class="num">198</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        showNotification(type = "warning", paste(</pre>
+                      <pre class="language-r">      assay = assay,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">124</td>
+                    <td class="num">199</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          "Excluded", ifelse(length(removed_assays) &gt; 1, "assays", "assay"),</pre>
+                      <pre class="language-r">      genes = genes,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">125</td>
+                    <td class="num">200</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">          hermes::h_short_list(removed_assays), "as per app specifications"</pre>
+                      <pre class="language-r">      probs = percentiles_without_borders</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">126</td>
+                    <td class="num">201</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        ))</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">127</td>
+                    <td class="num">202</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">128</td>
+                    <td class="num">203</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      if (length(remaining_assays) == 0) {</pre>
+                      <pre class="language-r">    km_plot &lt;- reactive({</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">129</td>
+                    <td class="num">204</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        remaining_assays &lt;- character(0)</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">130</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">      }</pre>
+                      <pre class="language-r">      strata_var &lt;- strata$sample_var()</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">131</td>
+                    <td class="num">205</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      remaining_assays</pre>
-                    </td>
-                  </tr>
-                  <tr class="never">
-                    <td class="num">132</td>
-                    <td class="coverage"></td>
-                    <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">      binned_adtte &lt;- adtte$binned_adtte_subset()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">133</td>
+                    <td class="num">206</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">134</td>
+                    <td class="num">207</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    observeEvent(choices(), {</pre>
+                      <pre class="language-r">      variables &lt;- list(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">135</td>
+                    <td class="num">208</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      choices &lt;- choices()</pre>
+                      <pre class="language-r">        tte = adtte_vars$aval,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">136</td>
+                    <td class="num">209</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      updateSelectizeInput(session, "name", choices = choices)</pre>
+                      <pre class="language-r">        is_event = adtte_vars$is_event,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">137</td>
+                    <td class="num">210</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      session$sendCustomMessage(</pre>
+                      <pre class="language-r">        arm = adtte$gene_factor,</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">138</td>
+                    <td class="num">211</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "toggle_dropdown",</pre>
+                      <pre class="language-r">        strat = strata_var</pre>
+                    </td>
+                  </tr>
+                  <tr class="never">
+                    <td class="num">212</td>
+                    <td class="coverage"></td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      )</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">139</td>
+                    <td class="num">213</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        list(input_id = session$ns("name"), disabled = (length(choices) == 0))</pre>
+                      <pre class="language-r">      tern::g_km(binned_adtte, variables = variables, annot_coxph = TRUE)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">140</td>
+                    <td class="num">214</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      )</pre>
+                      <pre class="language-r">    })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">141</td>
+                    <td class="num">215</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">216</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">    output$km_plot &lt;- renderPlot(km_plot())</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">142</td>
+                    <td class="num">217</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">143</td>
+                    <td class="num">218</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    reactive({</pre>
+                      <pre class="language-r">    pws &lt;- teal.widgets::plot_with_settings_srv(</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">144</td>
+                    <td class="num">219</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      choices &lt;- choices()</pre>
+                      <pre class="language-r">      id = "plot",</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">145</td>
+                    <td class="num">220</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      validate(need(</pre>
+                      <pre class="language-r">      plot_r = km_plot</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">146</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">221</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        length(choices) &gt; 0,</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
-                  <tr class="missed">
-                    <td class="num">147</td>
-                    <td class="coverage">!</td>
+                  <tr class="never">
+                    <td class="num">222</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">        "No assays eligible for this experiment, please make sure to add normalized assays"</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">148</td>
+                    <td class="num">223</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      ))</pre>
+                      <pre class="language-r">    ### REPORTER</pre>
                     </td>
                   </tr>
                   <tr class="missed">
-                    <td class="num">149</td>
+                    <td class="num">224</td>
                     <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">      input$name</pre>
+                      <pre class="language-r">    if (with_reporter) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">150</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">225</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    })</pre>
+                      <pre class="language-r">      card_fun &lt;- function(comment, label) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">151</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">226</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  })</pre>
+                      <pre class="language-r">        card &lt;- report_card_template(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">152</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">227</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          title = "Kaplan-Meier Plot",</pre>
                     </td>
                   </tr>
-                </tbody>
-              </table>
-            </div>
-            <div id="R/utils.R" class="hidden">
-              <table class="table-condensed">
-                <tbody>
-                  <tr class="never">
-                    <td class="num">1</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">228</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Checking for Empty String</pre>
+                      <pre class="language-r">          label = label,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">2</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">229</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          with_filter = TRUE,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">3</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">230</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge('experimental')`</pre>
+                      <pre class="language-r">          filter_panel_api = filter_panel_api</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">4</td>
+                    <td class="num">231</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">5</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">232</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This predicate function is helpful for functions where arguments could</pre>
+                      <pre class="language-r">        card$append_text("Selected Options", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">6</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">233</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' not yet be initialized from the teal module.</pre>
+                      <pre class="language-r">        encodings_list &lt;- list(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">7</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">234</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "Experiment:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">8</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">235</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x object to check.</pre>
+                      <pre class="language-r">          input$`experiment-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">9</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">236</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          "\nAssay:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">10</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">237</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Flag whether `x` is identical to an empty string, i.e. `""`.</pre>
+                      <pre class="language-r">          input$`assay-name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">11</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">238</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">          "\nGenes Selected:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">12</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">239</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          paste0(genes()$get_gene_labels(), collapse = ", "),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">13</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">240</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">          "\nGene Summary:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">14</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">241</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' is_blank("")</pre>
+                      <pre class="language-r">          input$`genes-fun_name`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">15</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">242</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' is_blank(" ")</pre>
+                      <pre class="language-r">          "\nEndpoint:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">16</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">243</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">is_blank &lt;- function(x) {</pre>
+                      <pre class="language-r">          input$`adtte-paramcd`,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">17</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">244</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  identical(x, "")</pre>
+                      <pre class="language-r">          "\nStrata Selected:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">18</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">245</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">          input$`strata-sample_var`,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">19</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">246</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">          "\nQuantiles Displayed:",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">20</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">247</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Helper Function to Extract Words</pre>
+                      <pre class="language-r">          paste0(input$percentiles, collapse = "-")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">21</td>
+                    <td class="num">248</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        )</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">22</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">249</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @description `r lifecycle::badge("experimental")`</pre>
+                      <pre class="language-r">        null_encodings_indices &lt;- which(sapply(encodings_list, function(x) is.null(x) || x == ""))</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">23</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">250</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        final_encodings &lt;- if (length(null_encodings_indices) &gt; 0) {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">24</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">251</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' This helper function extracts words from a string. Here words are defined</pre>
+                      <pre class="language-r">          null_encodings_indices_1 &lt;- c(null_encodings_indices, null_encodings_indices - 1)</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">25</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">252</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' as containing lower or upper case letters, colons and dots. All other</pre>
+                      <pre class="language-r">          paste(encodings_list[-null_encodings_indices_1], collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">26</td>
+                    <td class="num">253</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' characters are considered separators.</pre>
+                      <pre class="language-r">        } else {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">27</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">254</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">          paste(encodings_list, collapse = " ")</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">28</td>
+                    <td class="num">255</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param x (`string`)\cr input.</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">29</td>
+                    <td class="num">256</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">30</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">257</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return Character vector with the extracted words.</pre>
+                      <pre class="language-r">        card$append_text(final_encodings, style = "verbatim")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">31</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">258</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @export</pre>
+                      <pre class="language-r">        card$append_text("Plot", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">32</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">259</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">        card$append_plot(km_plot(), dim = pws$dim())</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">33</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">260</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @examples</pre>
+                      <pre class="language-r">        if (!comment == "") {</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">34</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">261</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' h_extract_words("a, b, , c, 234; 34562 - GeneID:bla")</pre>
+                      <pre class="language-r">          card$append_text("Comment", "header3")</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">35</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">262</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' h_extract_words("GeneID:1820, sdf.393; 32596")</pre>
+                      <pre class="language-r">          card$append_text(comment)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">36</td>
+                    <td class="num">263</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">h_extract_words &lt;- function(x) {</pre>
+                      <pre class="language-r">        }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">37</td>
-                    <td class="coverage">3<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">264</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  assert_string(x, min.chars = 1L)</pre>
+                      <pre class="language-r">        card</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">38</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">265</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  stringr::str_extract_all(</pre>
+                      <pre class="language-r">      }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">39</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">266</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    x,</pre>
+                      <pre class="language-r">      teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">40</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">267</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    "[a-zA-Z0-9:\\.]+"</pre>
+                      <pre class="language-r">    }</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">41</td>
-                    <td class="coverage">2<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">268</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )[[1]]</pre>
+                      <pre class="language-r">    ###</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">42</td>
+                    <td class="num">269</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">  })</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">43</td>
+                    <td class="num">270</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">}</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">44</td>
+                    <td class="num">271</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Include `CSS` files from `/inst/css/` package directory to application header</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">45</td>
+                    <td class="num">272</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' @describeIn tm_g_km sample module function.</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">46</td>
+                    <td class="num">273</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' `system.file` should not be used to access files in other packages, it does</pre>
+                      <pre class="language-r">#' @export</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">47</td>
+                    <td class="num">274</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' not work with `devtools`. Therefore, we redefine this method in each package</pre>
+                      <pre class="language-r">#' @examples</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">48</td>
+                    <td class="num">275</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' as needed. Thus, we do not export this method</pre>
+                      <pre class="language-r">#'</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">49</td>
+                    <td class="num">276</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#' # Alternatively you can run the sample module with this function call:</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">50</td>
+                    <td class="num">277</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param pattern (`character`) pattern of files to be included</pre>
+                      <pre class="language-r">#' if (interactive()) {</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">51</td>
+                    <td class="num">278</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">#'   sample_tm_g_km()</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">52</td>
+                    <td class="num">279</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return HTML code that includes `CSS` files</pre>
+                      <pre class="language-r">#' }</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">53</td>
+                    <td class="num">280</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @keywords internal</pre>
+                      <pre class="language-r">sample_tm_g_km &lt;- function() { # nolint</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">54</td>
+                    <td class="num">281</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">include_css_files &lt;- function(pattern = "*") { # nolint</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">55</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">282</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  css_files &lt;- list.files(</pre>
+                      <pre class="language-r">  mae &lt;- hermes::multi_assay_experiment</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">56</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">283</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    system.file("css", package = "teal.modules.hermes", mustWork = TRUE),</pre>
+                      <pre class="language-r">  adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">57</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">284</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pattern = pattern, full.names = TRUE</pre>
+                      <pre class="language-r">    dplyr::mutate(is_event = (.data$CNSR == 0))</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">58</td>
+                    <td class="num">285</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  )</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">59</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">286</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  return(shiny::singleton(shiny::tags$head(lapply(css_files, includeCSS))))</pre>
+                      <pre class="language-r">  data &lt;- teal.data::teal_data(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">60</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">287</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">}</pre>
+                      <pre class="language-r">    teal.data::dataset(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">61</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">288</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r"></pre>
+                      <pre class="language-r">      "ADTTE",</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">62</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">289</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' Include `JS` files from `/inst/js/` package directory to application header</pre>
+                      <pre class="language-r">      adtte,</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">63</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">290</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">      code = "adtte &lt;- teal.modules.hermes::rADTTE %&gt;%</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">64</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">291</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' `system.file` should not be used to access files in other packages, it does</pre>
+                      <pre class="language-r">        dplyr::mutate(is_event = (.data$CNSR == 0))"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">65</td>
+                    <td class="num">292</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' not work with `devtools`. Therefore, we redefine this method in each package</pre>
+                      <pre class="language-r">    ),</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">66</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">293</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' as needed. Thus, we do not export this method</pre>
+                      <pre class="language-r">    teal.data::dataset("MAE", mae)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">67</td>
+                    <td class="num">294</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">68</td>
+                    <td class="num">295</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param pattern (`character`) pattern of files to be included, passed to `system.file`</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">69</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">296</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @param except (`character`) vector of basename filenames to be excluded</pre>
+                      <pre class="language-r">  modules &lt;- teal::modules(</pre>
                     </td>
                   </tr>
-                  <tr class="never">
-                    <td class="num">70</td>
-                    <td class="coverage"></td>
+                  <tr class="missed">
+                    <td class="num">297</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#'</pre>
+                      <pre class="language-r">    tm_g_km(</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">298</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      label = "kaplan-meier",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">299</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      adtte_name = "ADTTE",</pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">300</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">      mae_name = "MAE"</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">71</td>
+                    <td class="num">301</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @return HTML code that includes `JS` files</pre>
+                      <pre class="language-r">    )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">72</td>
+                    <td class="num">302</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">#' @keywords internal</pre>
+                      <pre class="language-r">  )</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">73</td>
+                    <td class="num">303</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">include_js_files &lt;- function(pattern = "*") { # nolint</pre>
+                      <pre class="language-r"></pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">74</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">304</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  js_files &lt;- list.files(</pre>
+                      <pre class="language-r">  app &lt;- teal::init(</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">75</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">305</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    system.file("js", package = "teal.modules.hermes", mustWork = TRUE),</pre>
+                      <pre class="language-r">    data = data,</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">76</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="missed">
+                    <td class="num">306</td>
+                    <td class="coverage">!</td>
                     <td class="col-sm-12">
-                      <pre class="language-r">    pattern = pattern, full.names = TRUE</pre>
+                      <pre class="language-r">    modules = modules</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">77</td>
+                    <td class="num">307</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">  )</pre>
                     </td>
                   </tr>
-                  <tr class="covered">
-                    <td class="num">78</td>
-                    <td class="coverage">12<em>x</em></td>
+                  <tr class="never">
+                    <td class="num">308</td>
+                    <td class="coverage"></td>
                     <td class="col-sm-12">
-                      <pre class="language-r">  return(singleton(lapply(js_files, includeScript)))</pre>
+                      <pre class="language-r"></pre>
+                    </td>
+                  </tr>
+                  <tr class="missed">
+                    <td class="num">309</td>
+                    <td class="coverage">!</td>
+                    <td class="col-sm-12">
+                      <pre class="language-r">  shinyApp(ui = app$ui, server = app$server)</pre>
                     </td>
                   </tr>
                   <tr class="never">
-                    <td class="num">79</td>
+                    <td class="num">310</td>
                     <td class="coverage"></td>
                     <td class="col-sm-12">
                       <pre class="language-r">}</pre>