BUG: evaluate-busco brakes when input mags > ~1,300

q2_moshpit/assets/busco/index.html

@@ -33,16 +33,16 @@
 
 <div class="row row-cols-1 row-cols-md-2 g-4">
   <div class="col-lg-12">
-    <div class="card mt-3 h-100">
+    <div class="card mt-3 h-10">
       <h5 class="card-header">Plot description</h5>
       <div class="card-body">
         <p>
           The left plot shows the results generated by BUSCO for <b>all bins</b> and
           <b> samples</b>. "BUSCO attempts to provide a quantitative assessment
           of the completeness in terms of the expected gene content of a genome
           assembly, transcriptome, or annotated gene set. The results are
-          simplified into categories of Complete and single-copy, Complete and
-          duplicated, Fragmented, or Missing BUSCOs. BUSCO completeness results
+          simplified into categories of complete and single-copy, complete and
+          duplicated, fragmented, or missing BUSCOs. BUSCO completeness results
           make sense only in the context of the biology of your organism". Visit the 
           <a
             href="https://busco.ezlab.org/busco_userguide.html#interpreting-the-results"
@@ -51,10 +51,6 @@ <h5 class="card-header">Plot description</h5>
           >
           for more information. 
         </p>
-        <p>
-          Hoover over the graph to obtain information about the lineage dataset
-          used for each bin, and the number of genes in each BUSCO category.
-        </p>
         <p>
           The right barplot shows assembly statistics calculated for each bin using BBTools.
           Specifically, it displays the statistics computed by the <b>stats.sh</b> procedure from BBMap.
@@ -66,10 +62,6 @@ <h5 class="card-header">Plot description</h5>
           </a>
           of stats.sh for more information.
         </p>
-        <p>
-          Choose the assembly statistic that you wish to display from the drop-down manu below the graphs.
-          Hoover over the graph to show the numerical values that each bar represents.
-        </p>
 
         <div style="align-items: center; display: flex">
           <span class="header-inline">Downloads</span>
@@ -92,14 +84,46 @@ <h5 class="card-header">Plot description</h5>
         </div>
       </div>
     </div>
+
+    <div class="card mt-3 h-10">
+      <h5 class="card-header">Plot Controls</h5>
+      <div class="card-body">
+        <ul>
+          <li>
+            By default only the first 10 samples are displayed. Use a regular expression (regex) in the search box to display 
+            an arbitrary subset of the samples. 
+          </li>
+            <ul>
+              <li>
+                No more than ~1,300 MAGs can be displayed simultaneously. If you exceed this limit an error image will be displayed. 
+              </li>
+              <li>
+                If you have 14 samples named "sample_i" where "i" is a number from 1-14, and you whish to visualize only 
+                "sample_1" and "sample_14" your regex expression could look like this: ^sample_1$|^sample_14$
+              </li>
+              <li>
+                You can test your regex'es with this <a href="https://regex101.com/">Regular Expression Tester</a>.
+              </li>
+            </ul>
+          <li>
+            Choose the assembly statistic that you wish to display from the drop-down menu below.
+          </li>
+          <li>
+            Hover over the graph to obtain information about the lineage dataset
+            used for each bin, and the number of genes in each BUSCO category.
+          </li>
+        </ul>
+
+        <div id="plot-controls"></div>
+      </div>
+    </div>
   </div>
 </div>
 
 <div class="row">
   {% if vega_plots_overview is defined %}
   <div class="col-lg-6">
     <div id="plot"></div>
-    <div id="plot-controls"></div>
   </div>
   {% else %}
   <p>Unable to generate the completeness plot</p>
@@ -118,19 +142,21 @@ <h5 class="card-header">Plot description</h5>
 
     const spec = JSON.parse(document.getElementById("spec").innerHTML);
 
-    vegaEmbed("#plot", spec)
-      .then(function (result) {
-        result.view.logLevel(vega.Warn);
-        window.v = result.view;
+    vegaEmbed("#plot", spec).then(
+      function (result) {
+          result.view.logLevel(vega.Warn);
+          window.v = result.view;
 
-        // move the sliders to the right
-        const controls = document.getElementsByClassName("vega-bindings");
-        document.getElementById("plot-controls").appendChild(controls[0]);
-      })
-      .catch(function (error) {
-        // From 'js-error-handler.html'
-        handleErrors([error], $("#plot"));
-      });
+          // move the sliders to the right
+          const controls = document.getElementsByClassName("vega-bindings");
+          document.getElementById("plot-controls").appendChild(controls[0]);
+        }
+      ).catch(
+        function (error) {
+          // From 'js-error-handler.html'
+          handleErrors([error], $("#plot"));
+        }
+      );
   });
 </script>