diff --git a/main/404.html b/main/404.html
index 4fe715ae..0d844887 100644
--- a/main/404.html
+++ b/main/404.html
@@ -25,7 +25,7 @@
     
     <a class="navbar-brand me-2" href="https://insightsengineering.github.io/teal.modules.hermes/index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -43,15 +43,6 @@
 <li class="nav-item">
   <a class="nav-link" href="https://insightsengineering.github.io/teal.modules.hermes/news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul>
 <form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
diff --git a/main/CODE_OF_CONDUCT.html b/main/CODE_OF_CONDUCT.html
index 58e91b53..604aacd6 100644
--- a/main/CODE_OF_CONDUCT.html
+++ b/main/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/CONTRIBUTING.html b/main/CONTRIBUTING.html
index 9df3622b..869c90ca 100644
--- a/main/CONTRIBUTING.html
+++ b/main/CONTRIBUTING.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/LICENSE-text.html b/main/LICENSE-text.html
index 4ace35d5..8d2c8aac 100644
--- a/main/LICENSE-text.html
+++ b/main/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/SECURITY.html b/main/SECURITY.html
index e120217b..e9358886 100644
--- a/main/SECURITY.html
+++ b/main/SECURITY.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/articles/Getting_Started.html b/main/articles/Getting_Started.html
index a4ac7584..dfcffb86 100644
--- a/main/articles/Getting_Started.html
+++ b/main/articles/Getting_Started.html
@@ -27,7 +27,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -45,15 +45,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul>
 <form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
diff --git a/main/articles/index.html b/main/articles/index.html
index 00ed93ee..0938dc64 100644
--- a/main/articles/index.html
+++ b/main/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/authors.html b/main/authors.html
index becf942f..233e8e13 100644
--- a/main/authors.html
+++ b/main/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -130,13 +121,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2023).
 <em>teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application</em>.
-R package version 0.1.5.9006, <a href="https://github.com/insightsengineering/teal.modules.hermes/" class="external-link">https://github.com/insightsengineering/teal.modules.hermes/</a>. 
+R package version 0.1.5.9007, <a href="https://github.com/insightsengineering/teal.modules.hermes/" class="external-link">https://github.com/insightsengineering/teal.modules.hermes/</a>. 
 </p>
       <pre>@Manual{,
   title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application},
   author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang},
   year = {2023},
-  note = {R package version 0.1.5.9006},
+  note = {R package version 0.1.5.9007},
   url = {https://github.com/insightsengineering/teal.modules.hermes/},
 }</pre>
     </div>
diff --git a/main/index.html b/main/index.html
index 6e6fd4c1..e339f2a8 100644
--- a/main/index.html
+++ b/main/index.html
@@ -27,7 +27,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -45,15 +45,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul>
 <form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off">
diff --git a/main/news/index.html b/main/news/index.html
index b6ed9859..f1b31114 100644
--- a/main/news/index.html
+++ b/main/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="active nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -57,14 +48,14 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="0.1.5.9006" id="tealmoduleshermes-0159006">teal.modules.hermes 0.1.5.9006<a class="anchor" aria-label="anchor" href="#tealmoduleshermes-0159006"></a></h2>
+<h2 class="pkg-version" data-toc-text="0.1.5.9007" id="tealmoduleshermes-0159007">teal.modules.hermes 0.1.5.9007<a class="anchor" aria-label="anchor" href="#tealmoduleshermes-0159007"></a></h2>
 <div class="section level4">
-<h4 id="miscellaneous-0-1-5-9006">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-1-5-9006"></a></h4>
+<h4 id="miscellaneous-0-1-5-9007">Miscellaneous<a class="anchor" aria-label="anchor" href="#miscellaneous-0-1-5-9007"></a></h4>
 <ul><li>Added placeholders for <code>assaySpec</code>, <code>adtteSpec</code> and <code>geneSpec</code> inputs when no option is selected.</li>
 <li>Disabled the select input for <code>assaySpec</code> and <code>adtteSpec</code> when there are no options available.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="enhancements-0-1-5-9006">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-1-5-9006"></a></h4>
+<h4 id="enhancements-0-1-5-9007">Enhancements<a class="anchor" aria-label="anchor" href="#enhancements-0-1-5-9007"></a></h4>
 <ul><li>Updated the documentation and vignettes with the new way of specifying data for <code><a href="https://insightsengineering.github.io/teal/reference/init.html" class="external-link">teal::init()</a></code>. The <code>data</code> argument accepts <code>teal_data</code> object.</li>
 </ul></div>
 </div>
diff --git a/main/pkgdown.yml b/main/pkgdown.yml
index 04a49a41..8f413c9e 100644
--- a/main/pkgdown.yml
+++ b/main/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
   Getting_Started: Getting_Started.html
-last_built: 2023-11-20T11:35Z
+last_built: 2023-11-30T21:21Z
 urls:
   reference: https://insightsengineering.github.io/teal.modules.hermes/reference
   article: https://insightsengineering.github.io/teal.modules.hermes/articles
diff --git a/main/pull_request_template.html b/main/pull_request_template.html
index b7fd66e0..39b0191f 100644
--- a/main/pull_request_template.html
+++ b/main/pull_request_template.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -27,15 +27,6 @@
 <li class="nav-item">
   <a class="nav-link" href="news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/adtteSpecInput.html b/main/reference/adtteSpecInput.html
index 9cb3b021..9dee905f 100644
--- a/main/reference/adtteSpecInput.html
+++ b/main/reference/adtteSpecInput.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/adtteSpecServer.html b/main/reference/adtteSpecServer.html
index 306df2f4..b537faab 100644
--- a/main/reference/adtteSpecServer.html
+++ b/main/reference/adtteSpecServer.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -37,15 +37,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/assaySpecInput.html b/main/reference/assaySpecInput.html
index 30f6b44c..58ca45e2 100644
--- a/main/reference/assaySpecInput.html
+++ b/main/reference/assaySpecInput.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/assaySpecServer.html b/main/reference/assaySpecServer.html
index 36fe6ea4..36d2cbd7 100644
--- a/main/reference/assaySpecServer.html
+++ b/main/reference/assaySpecServer.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/assert_adtte_vars.html b/main/reference/assert_adtte_vars.html
index bf3091f0..192e3eae 100644
--- a/main/reference/assert_adtte_vars.html
+++ b/main/reference/assert_adtte_vars.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/assert_summary_funs.html b/main/reference/assert_summary_funs.html
index abe25d41..f460eb34 100644
--- a/main/reference/assert_summary_funs.html
+++ b/main/reference/assert_summary_funs.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/assertion_arguments.html b/main/reference/assertion_arguments.html
index 918ece1a..4583ac6f 100644
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diff --git a/main/reference/check_reactive.html b/main/reference/check_reactive.html
index 464fb65c..f7fb352a 100644
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diff --git a/main/reference/check_tag.html b/main/reference/check_tag.html
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index 276d88c5..b632bad9 100644
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diff --git a/main/reference/function_arguments.html b/main/reference/function_arguments.html
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diff --git a/main/reference/geneSpecInput.html b/main/reference/geneSpecInput.html
index 4653798c..786adb7e 100644
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@@ -12,7 +12,7 @@
     
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diff --git a/main/reference/geneSpecServer.html b/main/reference/geneSpecServer.html
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index 77ca2994..da5c0f6f 100644
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index ad485ac6..37544c9a 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
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index 790ad1f4..75f19b77 100644
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index 906b43da..e071b775 100644
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@@ -12,7 +12,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
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diff --git a/main/reference/h_order_genes.html b/main/reference/h_order_genes.html
index a5c980ca..71d517f7 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
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@@ -33,15 +33,6 @@
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diff --git a/main/reference/h_parse_genes.html b/main/reference/h_parse_genes.html
index 1b20c5c9..2b600a8c 100644
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@@ -14,7 +14,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
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     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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index 10d47334..77cdb598 100644
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@@ -16,7 +16,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
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     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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@@ -33,15 +33,6 @@
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diff --git a/main/reference/heatmap_plot.html b/main/reference/heatmap_plot.html
index 64fb71cd..7c57381c 100644
--- a/main/reference/heatmap_plot.html
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@@ -12,7 +12,7 @@
     
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     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
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index 98431859..411f66ae 100644
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index 78539dd5..308bdeff 100644
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index 24dc682f..2d7e0eaf 100644
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diff --git a/main/reference/sampleVarSpecServer.html b/main/reference/sampleVarSpecServer.html
index 4698706f..94b757fb 100644
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@@ -12,7 +12,7 @@
     
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/tm_g_barplot.html b/main/reference/tm_g_barplot.html
index d9a291f7..c9293039 100644
--- a/main/reference/tm_g_barplot.html
+++ b/main/reference/tm_g_barplot.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -171,7 +162,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:42.8379 pid:1278 token:[] teal.modules.hermes Initializing tm_g_barplot</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:02.9875 pid:1284 token:[] teal.modules.hermes Initializing tm_g_barplot</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_boxplot.html b/main/reference/tm_g_boxplot.html
index ba1dab7c..c9d76a18 100644
--- a/main/reference/tm_g_boxplot.html
+++ b/main/reference/tm_g_boxplot.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -171,7 +162,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:43.1538 pid:1278 token:[] teal.modules.hermes Initializing tm_g_boxplot</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:03.3175 pid:1284 token:[] teal.modules.hermes Initializing tm_g_boxplot</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_forest_tte.html b/main/reference/tm_g_forest_tte.html
index 92aab44c..9e5757f9 100644
--- a/main/reference/tm_g_forest_tte.html
+++ b/main/reference/tm_g_forest_tte.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -223,7 +214,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:43.4664 pid:1278 token:[] teal.modules.hermes Initializing tm_g_forest_tte</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:03.6290 pid:1284 token:[] teal.modules.hermes Initializing tm_g_forest_tte</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_km.html b/main/reference/tm_g_km.html
index f893bb8d..8c15a569 100644
--- a/main/reference/tm_g_km.html
+++ b/main/reference/tm_g_km.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -202,7 +193,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    mae_name <span class="op">=</span> <span class="st">"MAE"</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:44.0656 pid:1278 token:[] teal.modules.hermes Initializing tm_g_km</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:04.2513 pid:1284 token:[] teal.modules.hermes Initializing tm_g_km</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">app</span> <span class="op">&lt;-</span> <span class="fu">init</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  data <span class="op">=</span> <span class="va">data</span>,</span></span>
diff --git a/main/reference/tm_g_pca.html b/main/reference/tm_g_pca.html
index 94bea63c..af3a09c8 100644
--- a/main/reference/tm_g_pca.html
+++ b/main/reference/tm_g_pca.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,15 +33,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -158,7 +149,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:44.4251 pid:1278 token:[] teal.modules.hermes Initializing tm_g_pca</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:04.5832 pid:1284 token:[] teal.modules.hermes Initializing tm_g_pca</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_quality.html b/main/reference/tm_g_quality.html
index 0018bb3a..d87e5837 100644
--- a/main/reference/tm_g_quality.html
+++ b/main/reference/tm_g_quality.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -33,15 +33,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/tm_g_scatterplot.html b/main/reference/tm_g_scatterplot.html
index ff1b25f0..cc68afac 100644
--- a/main/reference/tm_g_scatterplot.html
+++ b/main/reference/tm_g_scatterplot.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
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         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -171,7 +162,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:44.9930 pid:1278 token:[] teal.modules.hermes Initializing tm_g_scatterplot</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:05.1668 pid:1284 token:[] teal.modules.hermes Initializing tm_g_scatterplot</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
diff --git a/main/reference/tm_g_volcanoplot.html b/main/reference/tm_g_volcanoplot.html
index f8398b58..70057f5b 100644
--- a/main/reference/tm_g_volcanoplot.html
+++ b/main/reference/tm_g_volcanoplot.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
@@ -162,7 +153,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-20 11:35:45.2765 pid:1278 token:[] teal.modules.hermes Initializing tm_g_volcanoplot</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [INFO] 2023-11-30 21:22:05.4534 pid:1284 token:[] teal.modules.hermes Initializing tm_g_volcanoplot</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">shinyApp</span><span class="op">(</span><span class="va">app</span><span class="op">$</span><span class="va">ui</span>, <span class="va">app</span><span class="op">$</span><span class="va">server</span><span class="op">)</span></span></span>
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diff --git a/main/reference/top_gene_plot.html b/main/reference/top_gene_plot.html
index a8dc632a..442710be 100644
--- a/main/reference/top_gene_plot.html
+++ b/main/reference/top_gene_plot.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -29,15 +29,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
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diff --git a/main/reference/validate_gene_spec.html b/main/reference/validate_gene_spec.html
index 9ae4e0c1..68f2d65c 100644
--- a/main/reference/validate_gene_spec.html
+++ b/main/reference/validate_gene_spec.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
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   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
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         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/reference/validate_n_levels.html b/main/reference/validate_n_levels.html
index 833ec132..ff7430ef 100644
--- a/main/reference/validate_n_levels.html
+++ b/main/reference/validate_n_levels.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">teal.modules.hermes</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9006</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.1.5.9007</small>
 
     <div style="width: 140px; margin-left: 0.5rem;"> <small class="nav-text text-muted me-auto">part of</small> <img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/nest.png?raw=true" alt="NEST" style="height: 30px;"><a href="https://pharmaverse.org/" class="external-link"><img src="https://github.com/insightsengineering/hex-stickers/blob/main/PNG/pharmaverse.png?raw=true" alt="pharmaverse" style="height: 28px;"></a> </div>
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -31,15 +31,6 @@
 <li class="nav-item">
   <a class="nav-link" href="../news/index.html">Changelog</a>
 </li>
-<!-- start dropdown for versions --> <li class="nav-item dropdown">
-        <a href="#" class="nav-link dropdown-toggle"
-          data-bs-toggle="dropdown" role="button"
-          aria-expanded="false" aria-haspopup="true"
-          id="dropdown-versions">Versions</a> <div class="dropdown-menu" aria-labelledby="dropdown-versions"> <a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/main">main</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/latest-tag">latest-tag</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.5">v0.1.5</a>
-<a class="dropdown-item" data-toggle="tooltip" title="" href="https://insightsengineering.github.io/teal.modules.hermes/v0.1.4">v0.1.4</a> </div></li>
-<!-- end dropdown for versions -->
       </ul><form class="form-inline my-2 my-lg-0" role="search">
         <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off"></form>
 
diff --git a/main/search.json b/main/search.json
index e13c8350..347132e6 100644
--- a/main/search.json
+++ b/main/search.json
@@ -1 +1 @@
-[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started","text":"teal.modules.hermes package implementing number teal modules exploration RNA-sequencing counts data. addition predefined modules, teal.modules.hermes enables quick easy ad-hoc module creation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"ad-hoc-module-example","dir":"Articles","previous_headings":"","what":"Ad-hoc module example","title":"Getting Started","text":"Let’s assume function awesome_plot() takes count matrix makes awesome plot . Now like make Shiny app can filter patients, samples, select experiment MultiAssayExperiment (MAE), select count matrix experiment, etc. Nothing easier teal.modules.hermes! show quickly spin UI, server put together nice little app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"ui-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"UI function","title":"Getting Started","text":"teal.modules.hermes provide modules make experiment assay selection super easy, see UI part:","code":"ui <- function(id,                data,                mae_name) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(ns(\"experiment\"), data, mae_name),       assaySpecInput(ns(\"assay\"))     ),     output = plotOutput(ns(\"awesome_plot\"))   ) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"server-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Server function","title":"Getting Started","text":"Similarly server use modules, call awesome plotting function.","code":"srv <- function(input,                 output,                 session,                 data,                 filter_panel_api,                 mae_name) {   experiment <- experimentSpecServer(     \"experiment\",     data = data,     filter_panel_api = filter_panel_api,     mae_name = mae_name,     name_annotation = NULL # If you have a gene name column in your rowData, can specify here.   )   assay <- assaySpecServer(\"assay\", experiment$assays)   output$awesome_plot <- renderPlot({     data <- experiment$data()     assay <- assay()     req(assay %in% SummarizedExperiment::assayNames(data))     counts <- SummarizedExperiment::assay(data, assay)     df <- data.frame(gene = rownames(counts), counts = rowSums(counts))     df <- na.omit(df[order(df$counts, decreasing = TRUE), ])     df$gene <- factor(df$gene, levels = df$gene)     df <- df[1:10, ]     ggplot(df, aes(x = gene, y = counts)) +       geom_col() +       theme(axis.text.x = element_text(angle = 90))   }) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"app-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"App function","title":"Getting Started","text":"Now let’s assume want spin app MAE.","code":"awesome_app <- function(mae, label = \"My awesome app\") {   mae_name <- \"MAE\"   mae <- hermes::lapply(mae, hermes::HermesData)   mae_data <- dataset(mae_name, mae)   data <- teal_data(mae_data)   app <- init(     data = data,     modules = teal::modules(       module(         label = label,         server = srv,         server_args = list(mae_name = mae_name),         ui = ui,         ui_args = list(mae_name = mae_name),         datanames = mae_name       )     )   )   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/articles/Getting_Started.html","id":"testing-it","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Testing it","title":"Getting Started","text":"test :","code":"awesome_app(hermes::multi_assay_experiment)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Nikolas Burkoff. Author. Dinakar Kulkarni. Author. Konrad Pagacz. Author. Namrata Bhatia. Author. Dawid Kaledkowski. Author. Pawel Rucki. Author. Jeff Luong. Author. Stefanie Bienert. Author. Haocheng Li. Author. Lyndsee Midori Zhang. Author. Sorin Voicu. Contributor. Benoit Falquet. Contributor. Mahmoud Hallal. Contributor. Tim Treis. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2023). teal.modules.hermes: RNA-Seq Analysis Modules Add Teal Application. R package version 0.1.5.9006, https://github.com/insightsengineering/teal.modules.hermes/.","code":"@Manual{,   title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application},   author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang},   year = {2023},   note = {R package version 0.1.5.9006},   url = {https://github.com/insightsengineering/teal.modules.hermes/}, }"},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"what-is-teal","dir":"","previous_headings":"What is what","what":"What is teal?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal shiny-based interactive exploration framework analyzing clinical trials data. teal currently provides dynamic filtering facility diverse data viewers. teal shiny applications built using standard shiny modules. See teal page details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"what-is-hermes","dir":"","previous_headings":"What is what","what":"What is hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data. core functionality built BioConductor ecosystem, especially SummarizedExperiment class HermesData class inherits. See vignette details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"so-what-is-then-tealmoduleshermes","dir":"","previous_headings":"What is what","what":"So what is then teal.modules.hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal.modules.hermes provides teal modules (can used part teal app), interactive RNA-seq data analysis using hermes. heavily built BioConductor classes, particular MultiAssayExperiment (MAE) expected contain HermesData experiments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"July 2023 insightsengineering packages available r-universe. See package vignettes browseVignettes(package = \"teal.modules.hermes\") usage package.","code":"# stable versions install.packages('teal.modules.hermes', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))  # beta versions install.packages('teal.modules.hermes', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/pull_request_template.html","id":null,"dir":"","previous_headings":"","what":"Pull Request","title":"Pull Request","text":"Fixes #nnn","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for ADTTE Specification — adtteSpecInput","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"defines input ADTTE specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"","code":"adtteSpecInput(inputId, label_paramcd = \"Select Endpoint\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"inputId (string) ID used call module input. label_paramcd (string) label endpoint (PARAMCD) selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for ADTTE Specification — adtteSpecServer","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"defines server part ADTTE specification. resulting data set binned_adtte_subset contains subset ADTTE selected time--event endpoint, joined together gene information extracted specified assay experiment, numeric factor columns. factor column created binning numeric column according quantile cutoffs specified probs.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"adtteSpecServer(   id,   data,   mae_name,   adtte_name,   adtte_vars,   experiment_data,   experiment_name,   assay,   genes,   probs )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. mae_name (string) name MAE data used teal module. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. experiment_data (reactive AnyHermesData) input experiment. experiment_name (reactive string) name input experiment. assay (reactive string) name assay. genes (reactive GeneSpec) gene specification. probs (reactive numeric) probabilities bin gene gene signature .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"List following elements: binned_adtte_subset: reactive containing joined ADTTE gene data. gene_col: reactive containing string column name original numeric gene variable. gene_factor: string variable name binned gene data. time_unit: reactive string time unit current subset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/adtteSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"ui <- function(id,                data) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(ns(\"experiment\"), data = data, mae_name = \"MAE\"),       assaySpecInput(ns(\"assay\")),       geneSpecInput(ns(\"genes\"), funs = list(Mean = colMeans)),       adtteSpecInput(ns(\"adtte\"))     ),     output = verbatimTextOutput(ns(\"summary\"))   ) }  server <- function(id, data, filter_panel_api) {   moduleServer(id, function(input, output, session) {     experiment <- experimentSpecServer(       \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       assays = experiment$assays     )     genes <- geneSpecServer(       \"genes\",       funs = list(Mean = colMeans),       gene_choices = experiment$genes     )     adtte <- adtteSpecServer(       \"adtte\",       data = data,       adtte_name = \"ADTTE\",       mae_name = \"MAE\",       adtte_vars = list(         aval = \"AVAL\",         avalu = \"AVALU\",         is_event = \"is_event\",         paramcd = \"PARAMCD\",         usubjid = \"USUBJID\"       ),       experiment_data = experiment$data,       experiment_name = experiment$name,       assay = assay,       genes = genes,       probs = reactive({         0.5       })     )     output$summary <- renderPrint({       binned_adtte_subset <- adtte$binned_adtte_subset()       summary(binned_adtte_subset)     })   }) }  my_app <- function() {   data <- teal_data()   data <- within(data, {     ADTTE <- teal.modules.hermes::rADTTE %>%       dplyr::mutate(is_event = .data$CNSR == 0)     MAE <- hermes::multi_assay_experiment   })   datanames <- c(\"ADTTE\", \"MAE\")   datanames(data) <- datanames   join_keys(data) <- default_cdisc_join_keys[datanames]    app <- init(     data = data,     modules = modules(       module(         label = \"adtteSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) }  if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Assay Specification — assaySpecInput","title":"Module Input for Assay Specification — assaySpecInput","text":"defines input assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Assay Specification — assaySpecInput","text":"","code":"assaySpecInput(inputId, label_assays = \"Select Assay\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Assay Specification — assaySpecInput","text":"inputId (string) ID used call module input. label_assays (string) label assay selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Assay Specification — assaySpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Assay Specification — assaySpecServer","title":"Module Server for Assay Specification — assaySpecServer","text":"defines server part assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"assaySpecServer(id, assays, exclude_assays = character())"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Assay Specification — assaySpecServer","text":"id (string) shiny module id. assays (reactive character) available assays currently selected experiment. exclude_assays (character) names assays included choices teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Assay Specification — assaySpecServer","text":"chosen assay reactive string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assaySpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"ui <- function(id,                data) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(         ns(\"experiment\"),         data,         \"MAE\"       ),       assaySpecInput(         ns(\"assay\"),         label_assays = \"Please choose assay\"       )     ),     output = textOutput(ns(\"result\"))   ) }  server <- function(id, data, filter_panel_api) {   moduleServer(id, module = function(input, output, session) {     experiment <- experimentSpecServer(       id = \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       experiment$assays,       exclude_assays = c(\"counts\", \"cpm\", \"tpm\", \"bla\")     )     output$result <- renderPrint({       assay()     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"assaySpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for ADTTE Variables — assert_adtte_vars","title":"Check for ADTTE Variables — assert_adtte_vars","text":"Check whether x list ADTTE variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for ADTTE Variables — assert_adtte_vars","text":"x object check.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_adtte_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(list(aval = \"AV\", is_event = \"EV\", paramcd = \"PC\", usubjid = \"ID\", avalu = \"u\"))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for List of Summary Functions — assert_summary_funs","title":"Check for List of Summary Functions — assert_summary_funs","text":"Check whether x list summary functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(x, null.ok = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for List of Summary Functions — assert_summary_funs","text":"x object check. null.ok (flag) whether x may also contain NULL, meaning user choice possible summary function applied.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assert_summary_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertion_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Assertion Arguments — assertion_arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"documentation function lists conventional arguments additional checkmate assertions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertion_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for checkmate — assertions","title":"Additional Assertions for checkmate — assertions","text":"provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for checkmate — assertions","text":"Depending function prefix. assert_ functions return object invisibly successful, otherwise throw error message. check_ functions return TRUE successful, otherwise string error message. test_ functions just return TRUE FALSE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Reactive Input — check_reactive","title":"Check for Reactive Input — check_reactive","text":"Check whether x reactive input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(x)  assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)  test_reactive(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Reactive Input — check_reactive","text":"x object check. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_reactive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(\"bla\") #> [1] FALSE check_reactive(reactive(\"bla\")) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Shiny Tag — check_tag","title":"Check for Shiny Tag — check_tag","text":"Check whether x shiny tag.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(x, null.ok = FALSE)  assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)  test_tag(x, null.ok = FALSE)  expect_tag(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Shiny Tag — check_tag","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/check_tag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(\"bla\") #> [1] \"Must be a 'shiny.tag' or NULL\" check_tag(NULL, null.ok = TRUE) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Experiment Specification — experimentSpecInput","title":"Module Input for Experiment Specification — experimentSpecInput","text":"defines input experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Experiment Specification — experimentSpecInput","text":"","code":"experimentSpecInput(   inputId,   data,   mae_name,   label_experiments = \"Select Experiment\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Experiment Specification — experimentSpecInput","text":"inputId (string) ID used call module input. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. mae_name (string) name MAE data used teal module. label_experiments (string) label experiment selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Experiment Specification — experimentSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Experiment Specification — experimentSpecServer","title":"Module Server for Experiment Specification — experimentSpecServer","text":"defines server part experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"experimentSpecServer(   id,   data,   filter_panel_api,   mae_name,   name_annotation = \"symbol\",   sample_vars_as_factors = TRUE,   with_mae_col_data = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Experiment Specification — experimentSpecServer","text":"id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. mae_name (string) name MAE data used teal module. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings. sample_vars_as_factors (flag) whether convert sample variables (columns colData() experiment) character factor variables. with_mae_col_data (flag) whether include colData() MAE experiment colData().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Experiment Specification — experimentSpecServer","text":"List following reactive objects: data: hermes::AnyHermesData experiment. name: name experiment selected user. genes: data.frame genes data, columns id name. assays: names assays data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/experimentSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"ui <- function(id,                data,                mae_name) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(         ns(\"my_experiment\"),         data,         mae_name,         label_experiments = \"Please choose experiment\"       ),       selectInput(         ns(\"property\"),         \"Please choose property\",         c(\"data\", \"name\", \"genes\", \"assays\")       )     ),     output = div(       verbatimTextOutput(ns(\"summary\")),       verbatimTextOutput(ns(\"head\"))     )   ) }  server <- function(id,                    data,                    filter_panel_api,                    mae_name) {   moduleServer(id, function(input, output, session) {     experiment <- experimentSpecServer(       \"my_experiment\",       data,       filter_panel_api,       mae_name     )     result <- reactive({       switch(input$property,         data = experiment$data(),         name = experiment$name(),         genes = experiment$genes(),         assays = experiment$assays()       )     })     output$summary <- renderPrint({       result <- result()       hermes::summary(result)     })     output$head <- renderPrint({       result <- result()       utils::head(result)     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"experimentSpec example\",         server = server,         server_args = list(mae_name = \"MAE\"),         ui = ui,         ui_args = list(mae_name = \"MAE\"),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/function_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Function Arguments — function_arguments","title":"Standard Function Arguments — function_arguments","text":"documentation function lists conventional arguments functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/function_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Function Arguments — function_arguments","text":"adtte (data frame) adtte dataset. usubjid_var (string) variable name subject ID variable. mae (MultiAssayExperiment) contains AnyHermesData objects. object (AnyHermesData) contains RNA-seq values one experiment. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Gene Signature Specification — geneSpecInput","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"defines input gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(   inputId,   funs,   label_genes = \"Select Gene(s)\",   label_funs = \"Select Gene Summary\",   label_text_button = \"Enter list of genes\",   label_lock_button =     \"Lock gene selection (so that it does not get updated when filtering)\",   label_select_all_button = paste0(\"Select All Genes (first \", max_options, \")\"),   label_select_none_button = \"Select None\",   max_options = 200L,   max_selected = max_options )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"inputId (string) ID used call module input. funs (named list) names list used function selection drop menu. label_genes (string) label gene selection. label_funs (string) label function selection. label_text_button (string) label text input button. label_lock_button (string) label lock button. label_select_all_button (string) label selecting genes button. label_select_none_button (string) label selecting genes button. max_options (count) maximum number gene options rendering selected via \"Select \". max_selected (count) maximum number genes can selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(\"my_genes\", list(mean = colMeans), label_funs = \"Please select function\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select Gene(s)<\/label> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_none_button\" title=\"Select None\" type=\"button\"> #>       <span> #>         <i aria-label=\"remove-circle icon\" class=\"glyphicon glyphicon-remove-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_all_button\" title=\"Select All Genes (first 200)\" type=\"button\"> #>       <span> #>         <i aria-label=\"ok-circle icon\" class=\"glyphicon glyphicon-ok-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-text_button\" title=\"Enter list of genes\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-font\" role=\"presentation\" aria-label=\"font icon\"><\/i> #>       <\/span> #>     <\/button> #>     <div class=\"pull-right\" title=\"Lock gene selection (so that it does not get updated when filtering)\"> #>       <div class=\"form-group shiny-input-container\"> #>         <div class=\"pretty p-toggle p-plain p-icon p-pulse\"> #>           <input id=\"my_genes-lock_button\" type=\"checkbox\"/> #>           <div class=\"state p-on\"> #>             <i aria-label=\"lock icon\" class=\"fas fa-lock icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>           <div class=\"state p-off\"> #>             <i aria-label=\"lock-open icon\" class=\"fas fa-lock-open icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>         <\/div> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label shiny-label-null\" for=\"my_genes-genes\" id=\"my_genes-genes-label\"><\/label> #>     <div> #>       <select class=\"shiny-input-select form-control\" id=\"my_genes-genes\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-genes\" data-eval=\"[&quot;render&quot;]\">{\"placeholder\":\"- Nothing selected -\",\"render\":\"{\\n          option: function(item, escape) {\\n              return '<div> <span style=\\\"font-size: inherit;\\\">' + item.label + '<\\/div>' +\\n                ' <span style=\\\"color: #808080; font-size: xx-small;\\\" >' + item.value + '<\\/div> <\\/div>'\\n            }\\n          }\",\"searchField\":[\"value\",\"label\"],\"maxOptions\":200,\"maxItems\":200,\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div> #> <div data-display-if=\"input.genes &amp;&amp; input.genes.length &gt; 1\" data-ns-prefix=\"my_genes-\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label\" id=\"my_genes-fun_name-label\" for=\"my_genes-fun_name\">Please select function<\/label> #>     <div> #>       <select id=\"my_genes-fun_name\" class=\"shiny-input-select\"><option value=\"mean\" selected>mean<\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-fun_name\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Gene Signature Specification — geneSpecServer","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"defines server part gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"geneSpecServer(   id,   funs,   gene_choices,   label_modal_title = \"Enter list of genes\",   label_modal_footer = c(\"Please enter a comma-separated list of gene IDs and/or names.\",     \"(Note that genes not included in current choices will be removed)\") )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"id (string) shiny module id. funs (static named list) names list used function selection drop menu. gene_choices (reactive data.frame) returns possible gene choices populate UI, data.frame columns id name. label_modal_title (string) title dialog asks text input. label_modal_footer (character) lines text use footer dialog.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"Reactive hermes::GeneSpec can used input relevant hermes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/geneSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"ui <- function(id,                data,                funs) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = div(       geneSpecInput(         ns(\"my_genes\"),         funs = funs,         label_funs = \"Please select function\"       )     ),     output = textOutput(ns(\"result\"))   ) } server <- function(id,                    data,                    funs) {   moduleServer(id, function(input, output, session) {     gene_choices <- reactive({       mae <- data[[\"MAE\"]]()       object <- mae[[1]]       gene_ids <- rownames(object)       gene_names <- SummarizedExperiment::rowData(object)$symbol       gene_data <- data.frame(         id = gene_ids,         name = gene_names       )       gene_data[order(gene_data$name), ]     })     gene_spec <- geneSpecServer(       \"my_genes\",       funs = funs,       gene_choices = gene_choices     )     output$result <- renderText({       validate_gene_spec(         gene_spec(),         gene_choices()$id       )       gene_spec <- gene_spec()       gene_spec$get_label()     })   }) } funs <- list(mean = colMeans) my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"GeneSpec example\",         server = server,         server_args = list(funs = funs),         ui = ui,         ui_args = list(funs = funs),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function For Group List Creation — h_assign_to_group_list","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"helper function takes assignment list converts group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"h_assign_to_group_list(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"x (named list character) input assignment list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"combination list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_assign_to_group_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"assign_list <- list(   \"ASIAN\" = \"1\",   \"BLACK OR AFRICAN AMERICAN\" = \"1\",   \"MULTIPLE\" = \"2\",   \"UNKNOWN\" = \"2\",   \"WHITE\" = \"4\" ) objective_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) result_list <- h_assign_to_group_list(assign_list) stopifnot(identical(result_list, objective_list))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"Given group list factor, helper function collapses levels factor accordingly also ensures resulting levels order given group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"h_collapse_levels(x, group_list)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"x (factor) original factor. group_list (named list character) includes collapsing specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"transformed factor x new levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_collapse_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"set.seed(123) x <- factor(sample(   c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"MULTIPLE\", \"UNKNOWN\", \"WHITE\"),   size = 30L,   replace = TRUE )) group_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) x_collapsed <- h_collapse_levels(x, group_list) stopifnot(identical(levels(x_collapsed), names(group_list)))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Extract Words — h_extract_words","title":"Helper Function to Extract Words — h_extract_words","text":"helper function extracts words string. words defined containing lower upper case letters, colons dots. characters considered separators.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Extract Words — h_extract_words","text":"x (string) input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Extract Words — h_extract_words","text":"Character vector extracted words.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_extract_words.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(\"a, b, , c, 234; 34562 - GeneID:bla\") #> [1] \"a\"          \"b\"          \"c\"          \"234\"        \"34562\"      #> [6] \"GeneID:bla\" h_extract_words(\"GeneID:1820, sdf.393; 32596\") #> [1] \"GeneID:1820\" \"sdf.393\"     \"32596\""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Format Gene Choices — h_gene_data","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Given hermes::AnyHermesData data object, well annotation column name use gene name, function formats contained genes data.frame ready consumption h_order_genes() e.g.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"h_gene_data(object, name_annotation)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Format Gene Choices — h_gene_data","text":"object (AnyHermesData) contains RNA-seq values one experiment. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Format Gene Choices — h_gene_data","text":"data.frame id name columns containing genes object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Note missing names names contain whitespace replaced empty strings consistency better labeling UI downstream","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_gene_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"object <- hermes::hermes_data[1:10, ] h_gene_data(object, \"symbol\") #>                  id         name #> 1      GeneID:11185         INMT #> 2      GeneID:10677         AVIL #> 3  GeneID:101928428 LOC101928428 #> 4  GeneID:100422835      MIR3183 #> 5  GeneID:102466731     MIR6769A #> 6      GeneID:64881       PCDH20 #> 7     GeneID:286205         SCAI #> 8       GeneID:8365     HIST1H4H #> 9       GeneID:6804        STX1A #> 10 GeneID:100423018    MIR3156-3"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"function help merging MAE ADTTE.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"h_km_mae_to_adtte(   adtte,   mae,   genes,   experiment_name = \"hd1\",   assay_name = \"counts\",   usubjid_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"adtte (data frame) adtte dataset. mae (MultiAssayExperiment) contains AnyHermesData objects. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups. usubjid_var (string) variable name subject ID variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"data frame containing columns/rows adtte match subject ID row names MAE gene samples available given experiment. attribute gene_cols contains column names gene columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"final gene column names can start different string original gene IDs (labels), particular white space colons removed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_km_mae_to_adtte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"mae <- hermes::multi_assay_experiment adtte <- teal.modules.hermes::rADTTE %>%   dplyr::mutate(CNSR = as.logical(CNSR))  new_adtte <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(\"GeneID:1820\"),   experiment_name = \"hd2\" ) new_adtte2 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(\"GeneID:1820\", \"GeneID:94115\"), fun = colMeans),   experiment_name = \"hd2\" ) new_adtte3 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(A = \"GeneID:1820\", B = \"GeneID:94115\")),   experiment_name = \"hd2\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Order Gene Choices — h_order_genes","title":"Helper Function to Order Gene Choices — h_order_genes","text":"possible gene choices ordered follows. First come genes non-empty name, ordered name alphabetically. Last come genes empty name, ordered ID alphabetically.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"h_order_genes(genes)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Order Gene Choices — h_order_genes","text":"genes (data.frame) containing id name columns gene choices. Note missing values allowed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Order Gene Choices — h_order_genes","text":"ordered data.frame.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_order_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"genes <- data.frame(   id = c(\"7\", \"1\", \"2\", \"345346\", \"0\"),   name = c(\"e\", \"\", \"c\", \"\", \"a\") ) h_order_genes(genes) #>       id name #> 5      0    a #> 3      2    c #> 1      7    e #> 2      1      #> 4 345346"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Parse Genes — h_parse_genes","title":"Helper Function to Parse Genes — h_parse_genes","text":"helper function takes vector words tries match id name columns possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(words, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Parse Genes — h_parse_genes","text":"words (character) containing gene IDs names. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Parse Genes — h_parse_genes","text":"subset choices matches words ID name.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_parse_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(   c(\"a\", \"2535\"),   data.frame(id = as.character(2533:2537), name = letters[1:5]) ) #>     id name #> 1 2533    a #> 3 2535    c"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_update_gene_selection.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Update Gene Selection — h_update_gene_selection","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"helper function takes intersection selected choices genes updates inputId accordingly. shows notification selected genes available.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_update_gene_selection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"","code":"h_update_gene_selection(session, inputId, selected, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/h_update_gene_selection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"session (ShinySession) session object. inputId (string) ID used call module input. selected (character) currently selected gene IDs. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation Heatmap Plot — heatmap_plot","title":"Correlation Heatmap Plot — heatmap_plot","text":"function plots correlation heatmap.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"heatmap_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation Heatmap Plot — heatmap_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation Heatmap Plot — heatmap_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/heatmap_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"library(hermes) #> Loading required package: ggfortify #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #>  #> Attaching package: ‘MatrixGenerics’ #> The following objects are masked from ‘package:matrixStats’: #>  #>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #>     colWeightedMeans, colWeightedMedians, colWeightedSds, #>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #>     rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #>  #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:stats’: #>  #>     IQR, mad, sd, var, xtabs #> The following objects are masked from ‘package:base’: #>  #>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #>     as.data.frame, basename, cbind, colnames, dirname, do.call, #>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, #>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, #>     tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #>  #> Attaching package: ‘S4Vectors’ #> The following object is masked from ‘package:utils’: #>  #>     findMatches #> The following objects are masked from ‘package:base’: #>  #>     I, expand.grid, unname #> Loading required package: IRanges #> Loading required package: GenomeInfoDb #>  #> Attaching package: ‘GenomicRanges’ #> The following object is masked from ‘package:magrittr’: #>  #>     subtract #> Loading required package: Biobase #> Welcome to Bioconductor #>  #>     Vignettes contain introductory material; view with #>     'browseVignettes()'. To cite Bioconductor, see #>     'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #>  #> Attaching package: ‘Biobase’ #> The following object is masked from ‘package:MatrixGenerics’: #>  #>     rowMedians #> The following objects are masked from ‘package:matrixStats’: #>  #>     anyMissing, rowMedians #>  #> Attaching package: ‘hermes’ #> The following object is masked from ‘package:stats’: #>  #>     filter object <- HermesData(summarized_experiment) result <- heatmap_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include CSS files from /inst/css/ package directory to application header — include_css_files","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"","code":"include_css_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"pattern (character) pattern files included","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_css_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"HTML code includes CSS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include JS files from /inst/js/ package directory to application header — include_js_files","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"","code":"include_js_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"pattern (character) pattern files included, passed system.file except (character) vector basename filenames excluded","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/include_js_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"HTML code includes JS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking for Empty String — is_blank","title":"Checking for Empty String — is_blank","text":"predicate function helpful functions arguments yet initialized teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking for Empty String — is_blank","text":"x object check.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking for Empty String — is_blank","text":"Flag whether x identical empty string, .e. \"\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/is_blank.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(\"\") #> [1] TRUE is_blank(\" \") #> [1] FALSE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/module_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Module Arguments — module_arguments","title":"Standard Module Arguments — module_arguments","text":"documentation function lists conventional arguments hermes teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/module_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Module Arguments — module_arguments","text":"data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. label (string) menu item label module teal app. inputId (string) ID used call module input. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . reporter (Reporter) object pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. filter_panel_api (FilterPanelAPI) object describing actual filter panel API.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"multiple sample variables used given module, wrapper makes much easier specify server function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"multiSampleVarSpecServer(inputIds, original_data, ...)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"inputIds (character) multiple input IDs corresponding different sample variables specified UI function. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. ... additional arguments documented sampleVarSpecServer(), namely mandatory experiment_name optional categorical_only, num_levels label_modal_title. transformed_data assign_lists specified already specified internally .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"List final transformed experiment_data reactive list vars contains selected sample variables reactives input ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/multiSampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"if (FALSE) { # In the server use: sample_var_specs <- multiSampleVarSpecServer(   inputIds = c(\"facet_var\", \"color_var\"),   experiment_name = reactive({     input$experiment_name   }),   original_data = ori_data # nolint Please update the <ori_data> ) # Then can extract the transformed data and selected variables later: experiment_data <- sample_var_specs$experiment_data() facet_var <- sample_var_specs$vars$facet_var() color_var <- sample_var_specs$vars$color_var() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Time to Event Analysis Dataset — rADTTE","title":"Random Time to Event Analysis Dataset — rADTTE","text":"Random Time Event Analysis Dataset","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Time to Event Analysis Dataset — rADTTE","text":"","code":"rADTTE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Time to Event Analysis Dataset — rADTTE","text":"object class tbl_df (inherits tbl, data.frame) 2000 rows 67 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/rADTTE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Time to Event Analysis Dataset — rADTTE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Sample Variable Specification — sampleVarSpecInput","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"defines input sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(   inputId,   label_vars = \"Select sample variable\",   label_levels_button = \"Combine factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"inputId (string) ID used call module input. label_vars (string) label sample variable selection. label_levels_button (string) label levels combination button.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(\"my_vars\", label_vars = \"Select faceting variable\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select faceting variable<\/label> #>   <\/div> #>   <div class=\"col-sm-4\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_vars-levels_button\" title=\"Combine factor levels\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-table\" role=\"presentation\" aria-label=\"table icon\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div> #>     <script> #>         $(function() { #>           $('#my_vars-sample_var').on('change', function(e) { #>             var select_concat = $(this).val().length ? $(this).val().join(', ') : 'NULL'; #>             $('#my_vars-sample_var_selected_text').html(select_concat); #>           }) #>         })<\/script> #>     <div> #>       <div id=\"my_vars-sample_var_input\" style=\"display: block;\"> #>         <div class=\"form-group shiny-input-container\"> #>           <label class=\"control-label shiny-label-null\" for=\"my_vars-sample_var\" id=\"my_vars-sample_var-label\"><\/label> #>           <select data-actions-box=\"false\" data-none-selected-text=\"- Nothing selected -\" data-max-options=\"1\" data-show-subtext=\"true\" data-live-search=\"false\" data-state-input=\"true\" id=\"my_vars-sample_var\" class=\"selectpicker form-control\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>         <\/div> #>       <\/div> #>       <div id=\"my_vars-sample_var_fixed\" style=\"display: none;\"> #>         <label class=\"control-label\"><\/label> #>         <code id=\"my_vars-sample_var_selected_text\">NULL<\/code> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Sample Variable Specification — sampleVarSpecServer","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"defines server part sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"sampleVarSpecServer(   id,   experiment_name,   original_data,   transformed_data = original_data,   assign_lists = reactiveValues(),   num_levels = NULL,   categorical_only = !is.null(num_levels),   explicit_na = FALSE,   label_modal_title = \"Please click to group the original factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"id (string) shiny module id. experiment_name (reactive string) name input experiment. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. transformed_data (reactive SummarizedExperiment) used multiple sample variables can selected app. case, pass pre-transformed data. assign_lists (reactivevalues) object share factor level groupings across multiple sample variables. num_levels (count NULL) required number levels combining original levels. NULL numbers levels allowed. categorical_only (flag) whether categorical variables selected . explicit_na (flag) whether colData original_data transformed hermes::h_df_factors_with_explicit_na processing. means also NA made explicit factor level counted num_levels. label_modal_title (string) title dialog asks text input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"Reactive SummarizedExperiment::SummarizedExperiment can used input relevant hermes functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"atomic columns (e.g. DataFrame columns) colData completely missing (NA) shown selection. num_levels specified factor columns available.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/sampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"ui <- function(id,                data) {   ns <- NS(id)   mae <- data[[\"MAE\"]]()   experiment_name_choices <- names(mae)   teal.widgets::standard_layout(     encoding = div(       selectInput(ns(\"experiment_name\"), \"Select experiment\", experiment_name_choices),       sampleVarSpecInput(ns(\"facet_var\"), \"Select faceting variable\")     ),     output = plotOutput(ns(\"plot\"))   ) } server <- function(id,                    data) {   moduleServer(id, function(input, output, session) {     experiment_data <- reactive({       req(input$experiment_name)       mae <- data[[\"MAE\"]]()       object <- mae[[input$experiment_name]]       SummarizedExperiment::colData(object) <-         hermes::df_cols_to_factor(SummarizedExperiment::colData(object))       object     })     facet_var_spec <- sampleVarSpecServer(       \"facet_var\",       experiment_name = reactive({         input$experiment_name       }),       original_data = experiment_data     )     output$plot <- renderPlot({       experiment_data_final <- facet_var_spec$experiment_data()       facet_var <- facet_var_spec$sample_var()       hermes::draw_boxplot(         experiment_data_final,         assay_name = \"counts\",         genes = hermes::gene_spec(hermes::genes(experiment_data_final)[1]),         facet_var = facet_var       )     })   }) } my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"sampleVarSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/teal.modules.hermes-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.modules.hermes Package — teal.modules.hermes-package","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"teal.modules.hermes provides RNA-seq analysis modules add teal application.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/teal.modules.hermes-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com Authors: Nikolas Burkoff Dinakar Kulkarni Konrad Pagacz Namrata Bhatia Dawid Kaledkowski Pawel Rucki Jeff Luong Stefanie Bienert Haocheng Li Lyndsee Midori Zhang contributors: Sorin Voicu [contributor] Benoit Falquet [contributor] Mahmoud Hallal [contributor] Tim Treis [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Barplot — tm_g_barplot","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"module provides interactive barplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"tm_g_barplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_barplot(id, data, mae_name, summary_funs, pre_output, post_output)  srv_g_barplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs )  sample_tm_g_barplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"ui_g_barplot(): sets user interface. srv_g_barplot(): sets server reactive graph. sample_tm_g_barplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_barplot(       label = \"barplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-20 11:35:42.8379 pid:1278 token:[] teal.modules.hermes Initializing tm_g_barplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_barplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"module provides interactive boxplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"tm_g_boxplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(None = NULL, Mean = colMeans, Median = matrixStats::colMedians, Max     = matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_boxplot(id, data, mae_name, summary_funs, pre_output, post_output)  srv_g_boxplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs )  sample_tm_g_boxplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"ui_g_boxplot(): sets user interface. srv_g_boxplot(): sets server reactive graph. sample_tm_g_boxplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_boxplot(       label = \"boxplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-20 11:35:43.1538 pid:1278 token:[] teal.modules.hermes Initializing tm_g_boxplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_boxplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Survival Forest Plot — tm_g_forest_tte","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"module provides interactive survival forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"tm_g_forest_tte(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   plot_height = c(600L, 200L, 2000L),   plot_width = c(1360L, 500L, 2000L) )  ui_g_forest_tte(   id,   data,   adtte_name,   mae_name,   summary_funs,   pre_output,   post_output )  srv_g_forest_tte(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   exclude_assays,   summary_funs,   plot_height,   plot_width )  sample_tm_g_forest_tte()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"ui_g_forest_tte(): sets user interface. srv_g_forest_tte(): sets server reactive graph. sample_tm_g_forest_tte(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_forest_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")  app <- init(   data = data,   modules = modules(     tm_g_forest_tte(       label = \"forestplot\",       adtte_name = \"ADTTE\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-20 11:35:43.4664 pid:1278 token:[] teal.modules.hermes Initializing tm_g_forest_tte if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_forest_tte() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Kaplan-Meier Plot — tm_g_km","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"teal module produces grid style Kaplan-Meier plot data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"tm_g_km(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_km(id, data, adtte_name, mae_name, summary_funs, pre_output, post_output)  srv_g_km(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   summary_funs,   exclude_assays )  sample_tm_g_km()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"ui_g_km(): sets user interface. srv_g_km(): sets user interface. sample_tm_g_km(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")   modules <- modules(   tm_g_km(     label = \"kaplan-meier\",     adtte_name = \"ADTTE\",     mae_name = \"MAE\"   ) ) #> [INFO] 2023-11-20 11:35:44.0656 pid:1278 token:[] teal.modules.hermes Initializing tm_g_km  app <- init(   data = data,   modules = modules )  if (interactive()) {   shinyApp(ui = app$ui, server = app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_km() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for PCA Analysis — tm_g_pca","title":"Teal Module for PCA Analysis — tm_g_pca","text":"module provides interactive principal components plot interactive heatmap correlation principal components sample variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"tm_g_pca(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL )  ui_g_pca(id, data, mae_name, pre_output, post_output)  srv_g_pca(id, data, filter_panel_api, reporter, mae_name, exclude_assays)  sample_tm_g_pca()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for PCA Analysis — tm_g_pca","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for PCA Analysis — tm_g_pca","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for PCA Analysis — tm_g_pca","text":"ui_g_pca(): sets user interface. srv_g_pca(): sets server reactive graph. sample_tm_g_pca(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_pca(       label = \"PCA plot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-20 11:35:44.4251 pid:1278 token:[] teal.modules.hermes Initializing tm_g_pca if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_pca() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Quality Control — tm_g_quality","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"module adds quality flags, filters genes /samples, normalizes AnyHermesData objects provides interactive plots RNA-seq gene expression quality control.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"tm_g_quality(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL )  ui_g_quality(id, data, mae_name, pre_output, post_output)  srv_g_quality(id, data, filter_panel_api, reporter, mae_name, exclude_assays)  sample_tm_g_quality()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"ui_g_quality(): sets user interface. srv_g_quality(): sets server reactive graphs. sample_tm_g_quality(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_quality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_quality(       label = \"Quality Control\",       mae_name = \"MAE\"     )   ) ) if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_quality() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"module provides interactive scatterplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"tm_g_scatterplot(   label,   mae_name,   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_scatterplot(id, data, mae_name, summary_funs, pre_output, post_output)  srv_g_scatterplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs )  sample_tm_g_scatterplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"ui_g_scatterplot(): sets user interface. srv_g_scatterplot(): sets server reactive graph. sample_tm_g_scatterplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_scatterplot(       label = \"scatterplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-20 11:35:44.9930 pid:1278 token:[] teal.modules.hermes Initializing tm_g_scatterplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_scatterplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"module provides interactive volcano plot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"tm_g_volcanoplot(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL )  ui_g_volcanoplot(id, data, mae_name, pre_output, post_output)  srv_g_volcanoplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays )  sample_tm_g_volcanoplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"ui_g_volcanoplot(): sets user interface. srv_g_volcanoplot(): sets server reactive graph. sample_tm_g_volcanoplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/tm_g_volcanoplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_volcanoplot(       label = \"volcanoplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-20 11:35:45.2765 pid:1278 token:[] teal.modules.hermes Initializing tm_g_volcanoplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_volcanoplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Most Expressed Genes Plot — top_gene_plot","title":"Most Expressed Genes Plot — top_gene_plot","text":"function plots expressed genes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"top_gene_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Most Expressed Genes Plot — top_gene_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Most Expressed Genes Plot — top_gene_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/top_gene_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"library(hermes) object <- HermesData(summarized_experiment) result <- top_gene_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_gene_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Gene Specification — validate_gene_spec","title":"Validation of Gene Specification — validate_gene_spec","text":"validation function checks given hermes::GeneSpec least one gene selected genes included possible choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_gene_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Gene Specification — validate_gene_spec","text":"","code":"validate_gene_spec(gene_spec, gene_choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_gene_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Gene Specification — validate_gene_spec","text":"gene_spec (GeneSpec) gene specification. gene_choices (character) possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_n_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Number of Levels — validate_n_levels","title":"Validation of Number of Levels — validate_n_levels","text":"validation function checks given vector x factor specified number levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_n_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Number of Levels — validate_n_levels","text":"","code":"validate_n_levels(x, name, n_levels)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/reference/validate_n_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Number of Levels — validate_n_levels","text":"x (factor) factor validate. name (string) name x app. n_levels (count) required number factor levels x.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-5-9006","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.5.9006","text":"Added placeholders assaySpec, adtteSpec geneSpec inputs option selected. Disabled select input assaySpec adtteSpec options available.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"enhancements-0-1-5-9006","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.hermes 0.1.5.9006","text":"Updated documentation vignettes new way specifying data teal::init(). data argument accepts teal_data object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"bug-fixes-0-1-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.5","text":"Filtering data filter panel now correctly triggers sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"breaking-changes-0-1-5","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.hermes 0.1.5","text":"Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.5","text":"Removed scda dependencies. Migrate shinytest2.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-014","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.4","title":"teal.modules.hermes 0.1.4","text":"Added teal.reporter functionality modules. Add installation instruction","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-013","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.3","title":"teal.modules.hermes 0.1.3","text":"Improve selection sample variables forest module (tm_g_forest_tte) categorical variables can selected first place.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.3","text":"Added template pkgdown site. Updated package authors. Added option categorical_only sampleVarSpec server module, allows show categorical sample variables selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-012","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.2","title":"teal.modules.hermes 0.1.2","text":"Rewrote modules use moduleServer updated call plot_with_settings_srv changes teal.devel. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. Added basic logging modules. Fixed geneSpecInput hermes app doesn’t fail anymore (chrome) experiment genes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"bug-fixes-0-1-1","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.1","text":"Updated legend PCA plot. Gene selection thousand genes longer hangs application. achieved different selection input corresponding geneSpec shiny module. atomic columns colData least one value can now selected sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.1","text":"Updated R version requirement >= 3.6. Updated sampleVarSpec geneSpec modules new icons remove warnings using shiny version >= 1.7. Removed dependencies deprecated packages utils.nest test.nest.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"tealmoduleshermes-010","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.0","title":"teal.modules.hermes 0.1.0","text":"First release teal.modules.hermes package, contains teal modules RNA-seq analysis using hermes package. New users first begin reading README.md teal.modules.hermes package become familiar.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/main/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.modules.hermes 0.1.0","text":"tm_g_barplot barplot module RNA-seq gene expression analysis. tm_g_boxplot boxplot module RNA-seq gene expression analysis. tm_g_forest_tte survival forest plot module analyze RNA-seq gene expression data together survival data. tm_g_km Kaplan-Meier plot module analyze RNA-seq gene expression data together survival data. tm_g_pca principal components analysis plot module RNA-seq gene expression analysis. tm_g_quality quality control module RNA-seq gene expression data. tm_g_scatterplot scatterplot module RNA-seq gene expression analysis. tm_g_volcanoplot differential gene expression analysis module.","code":""}]
+[{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"our-pledge","dir":"","previous_headings":"","what":"Our Pledge","title":"Contributor Covenant Code of Conduct","text":"members, contributors, leaders pledge make participation community harassment-free experience everyone, regardless age, body size, visible invisible disability, ethnicity, sex characteristics, gender identity expression, level experience, education, socio-economic status, nationality, personal appearance, race, caste, color, religion, sexual identity orientation. pledge act interact ways contribute open, welcoming, diverse, inclusive, healthy community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"our-standards","dir":"","previous_headings":"","what":"Our Standards","title":"Contributor Covenant Code of Conduct","text":"Examples behavior contributes positive environment community include: Demonstrating empathy kindness toward people respectful differing opinions, viewpoints, experiences Giving gracefully accepting constructive feedback Accepting responsibility apologizing affected mistakes, learning experience Focusing best just us individuals, overall community Examples unacceptable behavior include: use sexualized language imagery, sexual attention advances kind Trolling, insulting derogatory comments, personal political attacks Public private harassment Publishing others’ private information, physical email address, without explicit permission conduct reasonably considered inappropriate professional setting","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement-responsibilities","dir":"","previous_headings":"","what":"Enforcement Responsibilities","title":"Contributor Covenant Code of Conduct","text":"Community leaders responsible clarifying enforcing standards acceptable behavior take appropriate fair corrective action response behavior deem inappropriate, threatening, offensive, harmful. Community leaders right responsibility remove, edit, reject comments, commits, code, wiki edits, issues, contributions aligned Code Conduct, communicate reasons moderation decisions appropriate.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"scope","dir":"","previous_headings":"","what":"Scope","title":"Contributor Covenant Code of Conduct","text":"Code Conduct applies within community spaces, also applies individual officially representing community public spaces. Examples representing community include using official e-mail address, posting via official social media account, acting appointed representative online offline event.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement","dir":"","previous_headings":"","what":"Enforcement","title":"Contributor Covenant Code of Conduct","text":"Instances abusive, harassing, otherwise unacceptable behavior may reported community leaders responsible enforcement [INSERT CONTACT METHOD]. complaints reviewed investigated promptly fairly. community leaders obligated respect privacy security reporter incident.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"enforcement-guidelines","dir":"","previous_headings":"","what":"Enforcement Guidelines","title":"Contributor Covenant Code of Conduct","text":"Community leaders follow Community Impact Guidelines determining consequences action deem violation Code Conduct:","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_1-correction","dir":"","previous_headings":"Enforcement Guidelines","what":"1. Correction","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Use inappropriate language behavior deemed unprofessional unwelcome community. Consequence: private, written warning community leaders, providing clarity around nature violation explanation behavior inappropriate. public apology may requested.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_2-warning","dir":"","previous_headings":"Enforcement Guidelines","what":"2. Warning","title":"Contributor Covenant Code of Conduct","text":"Community Impact: violation single incident series actions. Consequence: warning consequences continued behavior. interaction people involved, including unsolicited interaction enforcing Code Conduct, specified period time. includes avoiding interactions community spaces well external channels like social media. Violating terms may lead temporary permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_3-temporary-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"3. Temporary Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: serious violation community standards, including sustained inappropriate behavior. Consequence: temporary ban sort interaction public communication community specified period time. public private interaction people involved, including unsolicited interaction enforcing Code Conduct, allowed period. Violating terms may lead permanent ban.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"id_4-permanent-ban","dir":"","previous_headings":"Enforcement Guidelines","what":"4. Permanent Ban","title":"Contributor Covenant Code of Conduct","text":"Community Impact: Demonstrating pattern violation community standards, including sustained inappropriate behavior, harassment individual, aggression toward disparagement classes individuals. Consequence: permanent ban sort public interaction within community.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CODE_OF_CONDUCT.html","id":"attribution","dir":"","previous_headings":"","what":"Attribution","title":"Contributor Covenant Code of Conduct","text":"Code Conduct adapted Contributor Covenant, version 2.1, available https://www.contributor-covenant.org/version/2/1/code_of_conduct.html. Community Impact Guidelines inspired Mozilla’s code conduct enforcement ladder. answers common questions code conduct, see FAQ https://www.contributor-covenant.org/faq. Translations available https://www.contributor-covenant.org/translations.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contribution Guidelines","title":"Contribution Guidelines","text":"🙏 Thank taking time contribute! input deeply valued, whether issue, pull request, even feedback, regardless size, content scope.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"table-of-contents","dir":"","previous_headings":"","what":"Table of contents","title":"Contribution Guidelines","text":"👶 Getting started 📔 Code Conduct 🗃 License 📜 Issues 🚩 Pull requests 💻 Coding guidelines 🏆 Recognition model ❓ Questions","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"getting-started","dir":"","previous_headings":"","what":"Getting started","title":"Contribution Guidelines","text":"Please refer project documentation brief introduction. Please also see articles within project documentation additional information.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"code-of-conduct","dir":"","previous_headings":"","what":"Code of Conduct","title":"Contribution Guidelines","text":"Code Conduct governs project. Participants contributors expected follow rules outlined therein.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"license","dir":"","previous_headings":"","what":"License","title":"Contribution Guidelines","text":"contributions covered project’s license.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"issues","dir":"","previous_headings":"","what":"Issues","title":"Contribution Guidelines","text":"use GitHub track issues, feature requests, bugs. submitting new issue, please check issue already reported. issue already exists, please upvote existing issue 👍. new feature requests, please elaborate context benefit feature users, developers, relevant personas.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"github-flow","dir":"","previous_headings":"Pull requests","what":"GitHub Flow","title":"Contribution Guidelines","text":"repository uses GitHub Flow model collaboration. submit pull request: Create branch Please see branch naming convention . don’t write access repository, please fork . Make changes Make sure code passes checks imposed GitHub Actions well documented well tested unit tests sufficiently covering changes introduced Create pull request (PR) pull request description, please link relevant issue (), provide detailed description change, include assumptions. Address review comments, Post approval Merge PR write access. Otherwise, reviewer merge PR behalf. Pat back Congratulations! 🎉 now official contributor project! grateful contribution.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"branch-naming-convention","dir":"","previous_headings":"Pull requests","what":"Branch naming convention","title":"Contribution Guidelines","text":"Suppose changes related current issue current project; please name branch follows: <issue_id>_<short_description>. Please use underscore (_) delimiter word separation. example, 420_fix_ui_bug suitable branch name change resolving UI-related bug reported issue number 420 current project. change affects multiple repositories, please name branches follows: <issue_id>_<issue_repo>_<short description>. example, 69_awesomeproject_fix_spelling_error reference issue 69 reported project awesomeproject aims resolve one spelling errors multiple (likely related) repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"monorepo-and-stageddependencies","dir":"","previous_headings":"Pull requests","what":"monorepo and staged.dependencies","title":"Contribution Guidelines","text":"Sometimes might need change upstream dependent package(s) able submit meaningful change. using staged.dependencies functionality simulate monorepo behavior. dependency configuration already specified project’s staged_dependencies.yaml file. need name feature branches appropriately. exception branch naming convention described . Please refer staged.dependencies package documentation details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"coding-guidelines","dir":"","previous_headings":"","what":"Coding guidelines","title":"Contribution Guidelines","text":"repository follows unified processes standards adopted maintainers ensure software development carried consistently within teams cohesively across repositories.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"style-guide","dir":"","previous_headings":"Coding guidelines","what":"Style guide","title":"Contribution Guidelines","text":"repository follows standard tidyverse style guide uses lintr lint checks. Customized lint configurations available repository’s .lintr file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"dependency-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency management","title":"Contribution Guidelines","text":"Lightweight right weight. repository follows tinyverse recommedations limiting dependencies minimum.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"dependency-version-management","dir":"","previous_headings":"Coding guidelines","what":"Dependency version management","title":"Contribution Guidelines","text":"code compatible (!) historical versions given dependenct package, required specify minimal version DESCRIPTION file. particular: development version requires (imports) development version another package - required put abc (>= 1.2.3.9000).","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"r--package-versions","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"R & package versions","title":"Contribution Guidelines","text":"continuously test packages newest R version along recent dependencies CRAN BioConductor. recommend working environment also set way. can find details R version packages used R CMD check GitHub Action execution log - step prints R sessionInfo(). discover bugs older R versions older set dependencies, please create relevant bug reports.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"pre-commit","dir":"","previous_headings":"Coding guidelines > Recommended development environment & tools","what":"pre-commit","title":"Contribution Guidelines","text":"highly recommend use pre-commit tool combined R hooks pre-commit execute checks committing pushing changes. Pre-commit hooks already available repository’s .pre-commit-config.yaml file.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"recognition-model","dir":"","previous_headings":"","what":"Recognition model","title":"Contribution Guidelines","text":"mentioned previously, contributions deeply valued appreciated. contribution data available part repository insights, recognize significant contribution hence add contributor package authors list, following rules enforced: Minimum 5% lines code authored* (determined git blame query) top 5 contributors terms number commits lines added lines removed* *Excluding auto-generated code, including limited roxygen comments renv.lock files. package maintainer also reserves right adjust criteria recognize contributions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/CONTRIBUTING.html","id":"questions","dir":"","previous_headings":"","what":"Questions","title":"Contribution Guidelines","text":"questions regarding contribution guidelines, please contact package/repository maintainer.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/SECURITY.html","id":"reporting-security-issues","dir":"","previous_headings":"","what":"Reporting Security Issues","title":"Security Policy","text":"believe found security vulnerability repositories organization, please report us coordinated disclosure. Please report security vulnerabilities public GitHub issues, discussions, pull requests. Instead, please send email vulnerability.management[@]roche.com. Please include much information listed can help us better understand resolve issue: type issue (e.g., buffer overflow, SQL injection, cross-site scripting) Full paths source file(s) related manifestation issue location affected source code (tag/branch/commit direct URL) special configuration required reproduce issue Step--step instructions reproduce issue Proof--concept exploit code (possible) Impact issue, including attacker might exploit issue information help us triage report quickly.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/SECURITY.html","id":"data-security-standards-dss","dir":"","previous_headings":"","what":"Data Security Standards (DSS)","title":"Security Policy","text":"Please make sure reporting issues form bug, feature, pull request, sensitive information PII, PHI, PCI completely removed text attachments, including pictures videos.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"Getting Started","text":"teal.modules.hermes package implementing number teal modules exploration RNA-sequencing counts data. addition predefined modules, teal.modules.hermes enables quick easy ad-hoc module creation.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"ad-hoc-module-example","dir":"Articles","previous_headings":"","what":"Ad-hoc module example","title":"Getting Started","text":"Let’s assume function awesome_plot() takes count matrix makes awesome plot . Now like make Shiny app can filter patients, samples, select experiment MultiAssayExperiment (MAE), select count matrix experiment, etc. Nothing easier teal.modules.hermes! show quickly spin UI, server put together nice little app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"ui-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"UI function","title":"Getting Started","text":"teal.modules.hermes provide modules make experiment assay selection super easy, see UI part:","code":"ui <- function(id,                data,                mae_name) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(ns(\"experiment\"), data, mae_name),       assaySpecInput(ns(\"assay\"))     ),     output = plotOutput(ns(\"awesome_plot\"))   ) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"server-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Server function","title":"Getting Started","text":"Similarly server use modules, call awesome plotting function.","code":"srv <- function(input,                 output,                 session,                 data,                 filter_panel_api,                 mae_name) {   experiment <- experimentSpecServer(     \"experiment\",     data = data,     filter_panel_api = filter_panel_api,     mae_name = mae_name,     name_annotation = NULL # If you have a gene name column in your rowData, can specify here.   )   assay <- assaySpecServer(\"assay\", experiment$assays)   output$awesome_plot <- renderPlot({     data <- experiment$data()     assay <- assay()     req(assay %in% SummarizedExperiment::assayNames(data))     counts <- SummarizedExperiment::assay(data, assay)     df <- data.frame(gene = rownames(counts), counts = rowSums(counts))     df <- na.omit(df[order(df$counts, decreasing = TRUE), ])     df$gene <- factor(df$gene, levels = df$gene)     df <- df[1:10, ]     ggplot(df, aes(x = gene, y = counts)) +       geom_col() +       theme(axis.text.x = element_text(angle = 90))   }) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"app-function","dir":"Articles","previous_headings":"Ad-hoc module example","what":"App function","title":"Getting Started","text":"Now let’s assume want spin app MAE.","code":"awesome_app <- function(mae, label = \"My awesome app\") {   mae_name <- \"MAE\"   mae <- hermes::lapply(mae, hermes::HermesData)   mae_data <- dataset(mae_name, mae)   data <- teal_data(mae_data)   app <- init(     data = data,     modules = teal::modules(       module(         label = label,         server = srv,         server_args = list(mae_name = mae_name),         ui = ui,         ui_args = list(mae_name = mae_name),         datanames = mae_name       )     )   )   shinyApp(app$ui, app$server) }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/articles/Getting_Started.html","id":"testing-it","dir":"Articles","previous_headings":"Ad-hoc module example","what":"Testing it","title":"Getting Started","text":"test :","code":"awesome_app(hermes::multi_assay_experiment)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Daniel Sabanés Bové. Author, maintainer. Nikolas Burkoff. Author. Dinakar Kulkarni. Author. Konrad Pagacz. Author. Namrata Bhatia. Author. Dawid Kaledkowski. Author. Pawel Rucki. Author. Jeff Luong. Author. Stefanie Bienert. Author. Haocheng Li. Author. Lyndsee Midori Zhang. Author. Sorin Voicu. Contributor. Benoit Falquet. Contributor. Mahmoud Hallal. Contributor. Tim Treis. Contributor. F. Hoffmann-La Roche AG. Copyright holder, funder.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Sabanés Bové D, Burkoff N, Kulkarni D, Pagacz K, Bhatia N, Kaledkowski D, Rucki P, Luong J, Bienert S, Li H, Zhang L (2023). teal.modules.hermes: RNA-Seq Analysis Modules Add Teal Application. R package version 0.1.5.9007, https://github.com/insightsengineering/teal.modules.hermes/.","code":"@Manual{,   title = {teal.modules.hermes: RNA-Seq Analysis Modules to Add to a Teal Application},   author = {Daniel {Sabanés Bové} and Nikolas Burkoff and Dinakar Kulkarni and Konrad Pagacz and Namrata Bhatia and Dawid Kaledkowski and Pawel Rucki and Jeff Luong and Stefanie Bienert and Haocheng Li and Lyndsee Midori Zhang},   year = {2023},   note = {R package version 0.1.5.9007},   url = {https://github.com/insightsengineering/teal.modules.hermes/}, }"},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"what-is-teal","dir":"","previous_headings":"What is what","what":"What is teal?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal shiny-based interactive exploration framework analyzing clinical trials data. teal currently provides dynamic filtering facility diverse data viewers. teal shiny applications built using standard shiny modules. See teal page details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"what-is-hermes","dir":"","previous_headings":"What is what","what":"What is hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"hermes facilitates preprocessing, analyzing, reporting RNA-seq data. core functionality built BioConductor ecosystem, especially SummarizedExperiment class HermesData class inherits. See vignette details.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"so-what-is-then-tealmoduleshermes","dir":"","previous_headings":"What is what","what":"So what is then teal.modules.hermes?","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"teal.modules.hermes provides teal modules (can used part teal app), interactive RNA-seq data analysis using hermes. heavily built BioConductor classes, particular MultiAssayExperiment (MAE) expected contain HermesData experiments.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"RNA-Seq Analysis Modules to Add to a Teal Application","text":"July 2023 insightsengineering packages available r-universe. See package vignettes browseVignettes(package = \"teal.modules.hermes\") usage package.","code":"# stable versions install.packages('teal.modules.hermes', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))  # beta versions install.packages('teal.modules.hermes', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))"},{"path":[]},{"path":[]},{"path":[]},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/pull_request_template.html","id":null,"dir":"","previous_headings":"","what":"Pull Request","title":"Pull Request","text":"Fixes #nnn","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for ADTTE Specification — adtteSpecInput","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"defines input ADTTE specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"","code":"adtteSpecInput(inputId, label_paramcd = \"Select Endpoint\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"inputId (string) ID used call module input. label_paramcd (string) label endpoint (PARAMCD) selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for ADTTE Specification — adtteSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for ADTTE Specification — adtteSpecServer","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"defines server part ADTTE specification. resulting data set binned_adtte_subset contains subset ADTTE selected time--event endpoint, joined together gene information extracted specified assay experiment, numeric factor columns. factor column created binning numeric column according quantile cutoffs specified probs.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"adtteSpecServer(   id,   data,   mae_name,   adtte_name,   adtte_vars,   experiment_data,   experiment_name,   assay,   genes,   probs )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. mae_name (string) name MAE data used teal module. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. experiment_data (reactive AnyHermesData) input experiment. experiment_name (reactive string) name input experiment. assay (reactive string) name assay. genes (reactive GeneSpec) gene specification. probs (reactive numeric) probabilities bin gene gene signature .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"List following elements: binned_adtte_subset: reactive containing joined ADTTE gene data. gene_col: reactive containing string column name original numeric gene variable. gene_factor: string variable name binned gene data. time_unit: reactive string time unit current subset.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/adtteSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for ADTTE Specification — adtteSpecServer","text":"","code":"ui <- function(id,                data) {   ns <- NS(id)    teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(ns(\"experiment\"), data = data, mae_name = \"MAE\"),       assaySpecInput(ns(\"assay\")),       geneSpecInput(ns(\"genes\"), funs = list(Mean = colMeans)),       adtteSpecInput(ns(\"adtte\"))     ),     output = verbatimTextOutput(ns(\"summary\"))   ) }  server <- function(id, data, filter_panel_api) {   moduleServer(id, function(input, output, session) {     experiment <- experimentSpecServer(       \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       assays = experiment$assays     )     genes <- geneSpecServer(       \"genes\",       funs = list(Mean = colMeans),       gene_choices = experiment$genes     )     adtte <- adtteSpecServer(       \"adtte\",       data = data,       adtte_name = \"ADTTE\",       mae_name = \"MAE\",       adtte_vars = list(         aval = \"AVAL\",         avalu = \"AVALU\",         is_event = \"is_event\",         paramcd = \"PARAMCD\",         usubjid = \"USUBJID\"       ),       experiment_data = experiment$data,       experiment_name = experiment$name,       assay = assay,       genes = genes,       probs = reactive({         0.5       })     )     output$summary <- renderPrint({       binned_adtte_subset <- adtte$binned_adtte_subset()       summary(binned_adtte_subset)     })   }) }  my_app <- function() {   data <- teal_data()   data <- within(data, {     ADTTE <- teal.modules.hermes::rADTTE %>%       dplyr::mutate(is_event = .data$CNSR == 0)     MAE <- hermes::multi_assay_experiment   })   datanames <- c(\"ADTTE\", \"MAE\")   datanames(data) <- datanames   join_keys(data) <- default_cdisc_join_keys[datanames]    app <- init(     data = data,     modules = modules(       module(         label = \"adtteSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) }  if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Assay Specification — assaySpecInput","title":"Module Input for Assay Specification — assaySpecInput","text":"defines input assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Assay Specification — assaySpecInput","text":"","code":"assaySpecInput(inputId, label_assays = \"Select Assay\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Assay Specification — assaySpecInput","text":"inputId (string) ID used call module input. label_assays (string) label assay selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Assay Specification — assaySpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Assay Specification — assaySpecServer","title":"Module Server for Assay Specification — assaySpecServer","text":"defines server part assay specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"assaySpecServer(id, assays, exclude_assays = character())"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Assay Specification — assaySpecServer","text":"id (string) shiny module id. assays (reactive character) available assays currently selected experiment. exclude_assays (character) names assays included choices teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Assay Specification — assaySpecServer","text":"chosen assay reactive string.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assaySpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Assay Specification — assaySpecServer","text":"","code":"ui <- function(id,                data) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(         ns(\"experiment\"),         data,         \"MAE\"       ),       assaySpecInput(         ns(\"assay\"),         label_assays = \"Please choose assay\"       )     ),     output = textOutput(ns(\"result\"))   ) }  server <- function(id, data, filter_panel_api) {   moduleServer(id, module = function(input, output, session) {     experiment <- experimentSpecServer(       id = \"experiment\",       data = data,       filter_panel_api = filter_panel_api,       mae_name = \"MAE\"     )     assay <- assaySpecServer(       \"assay\",       experiment$assays,       exclude_assays = c(\"counts\", \"cpm\", \"tpm\", \"bla\")     )     output$result <- renderPrint({       assay()     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"assaySpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for ADTTE Variables — assert_adtte_vars","title":"Check for ADTTE Variables — assert_adtte_vars","text":"Check whether x list ADTTE variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for ADTTE Variables — assert_adtte_vars","text":"x object check.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_adtte_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for ADTTE Variables — assert_adtte_vars","text":"","code":"assert_adtte_vars(list(aval = \"AV\", is_event = \"EV\", paramcd = \"PC\", usubjid = \"ID\", avalu = \"u\"))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for List of Summary Functions — assert_summary_funs","title":"Check for List of Summary Functions — assert_summary_funs","text":"Check whether x list summary functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(x, null.ok = FALSE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for List of Summary Functions — assert_summary_funs","text":"x object check. null.ok (flag) whether x may also contain NULL, meaning user choice possible summary function applied.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assert_summary_funs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for List of Summary Functions — assert_summary_funs","text":"","code":"assert_summary_funs(list(mean = colMeans, raw = NULL), null.ok = TRUE)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertion_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Assertion Arguments — assertion_arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"documentation function lists conventional arguments additional checkmate assertions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertion_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Assertion Arguments — assertion_arguments","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertions.html","id":null,"dir":"Reference","previous_headings":"","what":"Additional Assertions for checkmate — assertions","title":"Additional Assertions for checkmate — assertions","text":"provide additional assertion functions can used together checkmate functions. described individual help pages linked .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/assertions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Additional Assertions for checkmate — assertions","text":"Depending function prefix. assert_ functions return object invisibly successful, otherwise throw error message. check_ functions return TRUE successful, otherwise string error message. test_ functions just return TRUE FALSE.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Reactive Input — check_reactive","title":"Check for Reactive Input — check_reactive","text":"Check whether x reactive input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(x)  assert_reactive(x, .var.name = checkmate::vname(x), add = NULL)  test_reactive(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Reactive Input — check_reactive","text":"x object check. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_reactive.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Reactive Input — check_reactive","text":"","code":"check_reactive(\"bla\") #> [1] FALSE check_reactive(reactive(\"bla\")) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":null,"dir":"Reference","previous_headings":"","what":"Check for Shiny Tag — check_tag","title":"Check for Shiny Tag — check_tag","text":"Check whether x shiny tag.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(x, null.ok = FALSE)  assert_tag(x, null.ok = FALSE, .var.name = checkmate::vname(x), add = NULL)  test_tag(x, null.ok = FALSE)  expect_tag(x, null.ok = FALSE, info = NULL, label = vname(x))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check for Shiny Tag — check_tag","text":"x object check. null.ok (flag) whether x may also NULL. .var.name (string) name checked object print assertions; defaults heuristic implemented checkmate::vname(). add (AssertCollection NULL) collection store assertion messages, see checkmate::AssertCollection. info (string) extra information included message testthat reporter, see testthat::expect_that(). label (string) name checked object print messages. Defaults heuristic implemented checkmate::vname().","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/check_tag.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check for Shiny Tag — check_tag","text":"","code":"check_tag(\"bla\") #> [1] \"Must be a 'shiny.tag' or NULL\" check_tag(NULL, null.ok = TRUE) #> [1] TRUE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Experiment Specification — experimentSpecInput","title":"Module Input for Experiment Specification — experimentSpecInput","text":"defines input experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Experiment Specification — experimentSpecInput","text":"","code":"experimentSpecInput(   inputId,   data,   mae_name,   label_experiments = \"Select Experiment\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Experiment Specification — experimentSpecInput","text":"inputId (string) ID used call module input. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. mae_name (string) name MAE data used teal module. label_experiments (string) label experiment selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Experiment Specification — experimentSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Experiment Specification — experimentSpecServer","title":"Module Server for Experiment Specification — experimentSpecServer","text":"defines server part experiment specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"experimentSpecServer(   id,   data,   filter_panel_api,   mae_name,   name_annotation = \"symbol\",   sample_vars_as_factors = TRUE,   with_mae_col_data = TRUE )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Experiment Specification — experimentSpecServer","text":"id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. mae_name (string) name MAE data used teal module. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings. sample_vars_as_factors (flag) whether convert sample variables (columns colData() experiment) character factor variables. with_mae_col_data (flag) whether include colData() MAE experiment colData().","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Experiment Specification — experimentSpecServer","text":"List following reactive objects: data: hermes::AnyHermesData experiment. name: name experiment selected user. genes: data.frame genes data, columns id name. assays: names assays data.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/experimentSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Experiment Specification — experimentSpecServer","text":"","code":"ui <- function(id,                data,                mae_name) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = div(       experimentSpecInput(         ns(\"my_experiment\"),         data,         mae_name,         label_experiments = \"Please choose experiment\"       ),       selectInput(         ns(\"property\"),         \"Please choose property\",         c(\"data\", \"name\", \"genes\", \"assays\")       )     ),     output = div(       verbatimTextOutput(ns(\"summary\")),       verbatimTextOutput(ns(\"head\"))     )   ) }  server <- function(id,                    data,                    filter_panel_api,                    mae_name) {   moduleServer(id, function(input, output, session) {     experiment <- experimentSpecServer(       \"my_experiment\",       data,       filter_panel_api,       mae_name     )     result <- reactive({       switch(input$property,         data = experiment$data(),         name = experiment$name(),         genes = experiment$genes(),         assays = experiment$assays()       )     })     output$summary <- renderPrint({       result <- result()       hermes::summary(result)     })     output$head <- renderPrint({       result <- result()       utils::head(result)     })   }) }  my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"experimentSpec example\",         server = server,         server_args = list(mae_name = \"MAE\"),         ui = ui,         ui_args = list(mae_name = \"MAE\"),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/function_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Function Arguments — function_arguments","title":"Standard Function Arguments — function_arguments","text":"documentation function lists conventional arguments functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/function_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Function Arguments — function_arguments","text":"adtte (data frame) adtte dataset. usubjid_var (string) variable name subject ID variable. mae (MultiAssayExperiment) contains AnyHermesData objects. object (AnyHermesData) contains RNA-seq values one experiment. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Gene Signature Specification — geneSpecInput","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"defines input gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(   inputId,   funs,   label_genes = \"Select Gene(s)\",   label_funs = \"Select Gene Summary\",   label_text_button = \"Enter list of genes\",   label_lock_button =     \"Lock gene selection (so that it does not get updated when filtering)\",   label_select_all_button = paste0(\"Select All Genes (first \", max_options, \")\"),   label_select_none_button = \"Select None\",   max_options = 200L,   max_selected = max_options )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"inputId (string) ID used call module input. funs (named list) names list used function selection drop menu. label_genes (string) label gene selection. label_funs (string) label function selection. label_text_button (string) label text input button. label_lock_button (string) label lock button. label_select_all_button (string) label selecting genes button. label_select_none_button (string) label selecting genes button. max_options (count) maximum number gene options rendering selected via \"Select \". max_selected (count) maximum number genes can selected.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Gene Signature Specification — geneSpecInput","text":"","code":"geneSpecInput(\"my_genes\", list(mean = colMeans), label_funs = \"Please select function\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select Gene(s)<\/label> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_none_button\" title=\"Select None\" type=\"button\"> #>       <span> #>         <i aria-label=\"remove-circle icon\" class=\"glyphicon glyphicon-remove-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-select_all_button\" title=\"Select All Genes (first 200)\" type=\"button\"> #>       <span> #>         <i aria-label=\"ok-circle icon\" class=\"glyphicon glyphicon-ok-circle\" role=\"presentation\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #>   <div class=\"col-sm-2\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_genes-text_button\" title=\"Enter list of genes\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-font\" role=\"presentation\" aria-label=\"font icon\"><\/i> #>       <\/span> #>     <\/button> #>     <div class=\"pull-right\" title=\"Lock gene selection (so that it does not get updated when filtering)\"> #>       <div class=\"form-group shiny-input-container\"> #>         <div class=\"pretty p-toggle p-plain p-icon p-pulse\"> #>           <input id=\"my_genes-lock_button\" type=\"checkbox\"/> #>           <div class=\"state p-on\"> #>             <i aria-label=\"lock icon\" class=\"fas fa-lock icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>           <div class=\"state p-off\"> #>             <i aria-label=\"lock-open icon\" class=\"fas fa-lock-open icon\" role=\"presentation\"><\/i> #>             <label> #>               <span><\/span> #>             <\/label> #>           <\/div> #>         <\/div> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label shiny-label-null\" for=\"my_genes-genes\" id=\"my_genes-genes-label\"><\/label> #>     <div> #>       <select class=\"shiny-input-select form-control\" id=\"my_genes-genes\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-genes\" data-eval=\"[&quot;render&quot;]\">{\"placeholder\":\"- Nothing selected -\",\"render\":\"{\\n          option: function(item, escape) {\\n              return '<div> <span style=\\\"font-size: inherit;\\\">' + item.label + '<\\/div>' +\\n                ' <span style=\\\"color: #808080; font-size: xx-small;\\\" >' + item.value + '<\\/div> <\\/div>'\\n            }\\n          }\",\"searchField\":[\"value\",\"label\"],\"maxOptions\":200,\"maxItems\":200,\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div> #> <div data-display-if=\"input.genes &amp;&amp; input.genes.length &gt; 1\" data-ns-prefix=\"my_genes-\"> #>   <div class=\"form-group shiny-input-container\"> #>     <label class=\"control-label\" id=\"my_genes-fun_name-label\" for=\"my_genes-fun_name\">Please select function<\/label> #>     <div> #>       <select id=\"my_genes-fun_name\" class=\"shiny-input-select\"><option value=\"mean\" selected>mean<\/option><\/select> #>       <script type=\"application/json\" data-for=\"my_genes-fun_name\" data-nonempty=\"\">{\"plugins\":[\"selectize-plugin-a11y\"]}<\/script> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Gene Signature Specification — geneSpecServer","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"defines server part gene signature specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"geneSpecServer(   id,   funs,   gene_choices,   label_modal_title = \"Enter list of genes\",   label_modal_footer = c(\"Please enter a comma-separated list of gene IDs and/or names.\",     \"(Note that genes not included in current choices will be removed)\") )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"id (string) shiny module id. funs (static named list) names list used function selection drop menu. gene_choices (reactive data.frame) returns possible gene choices populate UI, data.frame columns id name. label_modal_title (string) title dialog asks text input. label_modal_footer (character) lines text use footer dialog.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"Reactive hermes::GeneSpec can used input relevant hermes functions.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/geneSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Gene Signature Specification — geneSpecServer","text":"","code":"ui <- function(id,                data,                funs) {   ns <- NS(id)   teal.widgets::standard_layout(     encoding = div(       geneSpecInput(         ns(\"my_genes\"),         funs = funs,         label_funs = \"Please select function\"       )     ),     output = textOutput(ns(\"result\"))   ) } server <- function(id,                    data,                    funs) {   moduleServer(id, function(input, output, session) {     gene_choices <- reactive({       mae <- data[[\"MAE\"]]()       object <- mae[[1]]       gene_ids <- rownames(object)       gene_names <- SummarizedExperiment::rowData(object)$symbol       gene_data <- data.frame(         id = gene_ids,         name = gene_names       )       gene_data[order(gene_data$name), ]     })     gene_spec <- geneSpecServer(       \"my_genes\",       funs = funs,       gene_choices = gene_choices     )     output$result <- renderText({       validate_gene_spec(         gene_spec(),         gene_choices()$id       )       gene_spec <- gene_spec()       gene_spec$get_label()     })   }) } funs <- list(mean = colMeans) my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"GeneSpec example\",         server = server,         server_args = list(funs = funs),         ui = ui,         ui_args = list(funs = funs),         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function For Group List Creation — h_assign_to_group_list","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"helper function takes assignment list converts group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"h_assign_to_group_list(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"x (named list character) input assignment list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"combination list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_assign_to_group_list.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function For Group List Creation — h_assign_to_group_list","text":"","code":"assign_list <- list(   \"ASIAN\" = \"1\",   \"BLACK OR AFRICAN AMERICAN\" = \"1\",   \"MULTIPLE\" = \"2\",   \"UNKNOWN\" = \"2\",   \"WHITE\" = \"4\" ) objective_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) result_list <- h_assign_to_group_list(assign_list) stopifnot(identical(result_list, objective_list))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"Given group list factor, helper function collapses levels factor accordingly also ensures resulting levels order given group list.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"h_collapse_levels(x, group_list)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"x (factor) original factor. group_list (named list character) includes collapsing specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"transformed factor x new levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_collapse_levels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function for Collapsing of Factor Levels — h_collapse_levels","text":"","code":"set.seed(123) x <- factor(sample(   c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\", \"MULTIPLE\", \"UNKNOWN\", \"WHITE\"),   size = 30L,   replace = TRUE )) group_list <- list(   \"ASIAN/BLACK OR AFRICAN AMERICAN\" = c(\"ASIAN\", \"BLACK OR AFRICAN AMERICAN\"),   \"MULTIPLE/UNKNOWN\" = c(\"MULTIPLE\", \"UNKNOWN\"),   \"WHITE\" = \"WHITE\" ) x_collapsed <- h_collapse_levels(x, group_list) stopifnot(identical(levels(x_collapsed), names(group_list)))"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Extract Words — h_extract_words","title":"Helper Function to Extract Words — h_extract_words","text":"helper function extracts words string. words defined containing lower upper case letters, colons dots. characters considered separators.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Extract Words — h_extract_words","text":"x (string) input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Extract Words — h_extract_words","text":"Character vector extracted words.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_extract_words.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Extract Words — h_extract_words","text":"","code":"h_extract_words(\"a, b, , c, 234; 34562 - GeneID:bla\") #> [1] \"a\"          \"b\"          \"c\"          \"234\"        \"34562\"      #> [6] \"GeneID:bla\" h_extract_words(\"GeneID:1820, sdf.393; 32596\") #> [1] \"GeneID:1820\" \"sdf.393\"     \"32596\""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Format Gene Choices — h_gene_data","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Given hermes::AnyHermesData data object, well annotation column name use gene name, function formats contained genes data.frame ready consumption h_order_genes() e.g.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"h_gene_data(object, name_annotation)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Format Gene Choices — h_gene_data","text":"object (AnyHermesData) contains RNA-seq values one experiment. name_annotation (string NULL) annotation column use name return genes data. NULL, name column set empty strings.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Format Gene Choices — h_gene_data","text":"data.frame id name columns containing genes object.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Helper Function to Format Gene Choices — h_gene_data","text":"Note missing names names contain whitespace replaced empty strings consistency better labeling UI downstream","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_gene_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Format Gene Choices — h_gene_data","text":"","code":"object <- hermes::hermes_data[1:10, ] h_gene_data(object, \"symbol\") #>                  id         name #> 1      GeneID:11185         INMT #> 2      GeneID:10677         AVIL #> 3  GeneID:101928428 LOC101928428 #> 4  GeneID:100422835      MIR3183 #> 5  GeneID:102466731     MIR6769A #> 6      GeneID:64881       PCDH20 #> 7     GeneID:286205         SCAI #> 8       GeneID:8365     HIST1H4H #> 9       GeneID:6804        STX1A #> 10 GeneID:100423018    MIR3156-3"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"function help merging MAE ADTTE.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"h_km_mae_to_adtte(   adtte,   mae,   genes,   experiment_name = \"hd1\",   assay_name = \"counts\",   usubjid_var = \"USUBJID\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"adtte (data frame) adtte dataset. mae (MultiAssayExperiment) contains AnyHermesData objects. genes (GeneSpec) specification gene(s) (signature), e.g. using hermes::gene_spec(). experiment_name (string) desired HermesData use. assay_name (string) assay define groups. usubjid_var (string) variable name subject ID variable.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"data frame containing columns/rows adtte match subject ID row names MAE gene samples available given experiment. attribute gene_cols contains column names gene columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"final gene column names can start different string original gene IDs (labels), particular white space colons removed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_km_mae_to_adtte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Preprocessing for ADTTE Module — h_km_mae_to_adtte","text":"","code":"mae <- hermes::multi_assay_experiment adtte <- teal.modules.hermes::rADTTE %>%   dplyr::mutate(CNSR = as.logical(CNSR))  new_adtte <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(\"GeneID:1820\"),   experiment_name = \"hd2\" ) new_adtte2 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(\"GeneID:1820\", \"GeneID:94115\"), fun = colMeans),   experiment_name = \"hd2\" ) new_adtte3 <- h_km_mae_to_adtte(   adtte,   mae,   genes = hermes::gene_spec(c(A = \"GeneID:1820\", B = \"GeneID:94115\")),   experiment_name = \"hd2\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Order Gene Choices — h_order_genes","title":"Helper Function to Order Gene Choices — h_order_genes","text":"possible gene choices ordered follows. First come genes non-empty name, ordered name alphabetically. Last come genes empty name, ordered ID alphabetically.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"h_order_genes(genes)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Order Gene Choices — h_order_genes","text":"genes (data.frame) containing id name columns gene choices. Note missing values allowed.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Order Gene Choices — h_order_genes","text":"ordered data.frame.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_order_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Order Gene Choices — h_order_genes","text":"","code":"genes <- data.frame(   id = c(\"7\", \"1\", \"2\", \"345346\", \"0\"),   name = c(\"e\", \"\", \"c\", \"\", \"a\") ) h_order_genes(genes) #>       id name #> 5      0    a #> 3      2    c #> 1      7    e #> 2      1      #> 4 345346"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Parse Genes — h_parse_genes","title":"Helper Function to Parse Genes — h_parse_genes","text":"helper function takes vector words tries match id name columns possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(words, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Parse Genes — h_parse_genes","text":"words (character) containing gene IDs names. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Helper Function to Parse Genes — h_parse_genes","text":"subset choices matches words ID name.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_parse_genes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Helper Function to Parse Genes — h_parse_genes","text":"","code":"h_parse_genes(   c(\"a\", \"2535\"),   data.frame(id = as.character(2533:2537), name = letters[1:5]) ) #>     id name #> 1 2533    a #> 3 2535    c"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_update_gene_selection.html","id":null,"dir":"Reference","previous_headings":"","what":"Helper Function to Update Gene Selection — h_update_gene_selection","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"helper function takes intersection selected choices genes updates inputId accordingly. shows notification selected genes available.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_update_gene_selection.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"","code":"h_update_gene_selection(session, inputId, selected, choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/h_update_gene_selection.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Helper Function to Update Gene Selection — h_update_gene_selection","text":"session (ShinySession) session object. inputId (string) ID used call module input. selected (character) currently selected gene IDs. choices (data.frame) containing id name columns new choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Correlation Heatmap Plot — heatmap_plot","title":"Correlation Heatmap Plot — heatmap_plot","text":"function plots correlation heatmap.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"heatmap_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Correlation Heatmap Plot — heatmap_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Correlation Heatmap Plot — heatmap_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/heatmap_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Correlation Heatmap Plot — heatmap_plot","text":"","code":"library(hermes) #> Loading required package: ggfortify #> Loading required package: SummarizedExperiment #> Loading required package: MatrixGenerics #> Loading required package: matrixStats #>  #> Attaching package: ‘MatrixGenerics’ #> The following objects are masked from ‘package:matrixStats’: #>  #>     colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, #>     colCounts, colCummaxs, colCummins, colCumprods, colCumsums, #>     colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, #>     colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, #>     colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, #>     colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, #>     colWeightedMeans, colWeightedMedians, colWeightedSds, #>     colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, #>     rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, #>     rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, #>     rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, #>     rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, #>     rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, #>     rowWeightedMads, rowWeightedMeans, rowWeightedMedians, #>     rowWeightedSds, rowWeightedVars #> Loading required package: GenomicRanges #> Loading required package: stats4 #> Loading required package: BiocGenerics #>  #> Attaching package: ‘BiocGenerics’ #> The following objects are masked from ‘package:stats’: #>  #>     IQR, mad, sd, var, xtabs #> The following objects are masked from ‘package:base’: #>  #>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append, #>     as.data.frame, basename, cbind, colnames, dirname, do.call, #>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, #>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, #>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table, #>     tapply, union, unique, unsplit, which.max, which.min #> Loading required package: S4Vectors #>  #> Attaching package: ‘S4Vectors’ #> The following object is masked from ‘package:utils’: #>  #>     findMatches #> The following objects are masked from ‘package:base’: #>  #>     I, expand.grid, unname #> Loading required package: IRanges #> Loading required package: GenomeInfoDb #>  #> Attaching package: ‘GenomicRanges’ #> The following object is masked from ‘package:magrittr’: #>  #>     subtract #> Loading required package: Biobase #> Welcome to Bioconductor #>  #>     Vignettes contain introductory material; view with #>     'browseVignettes()'. To cite Bioconductor, see #>     'citation(\"Biobase\")', and for packages 'citation(\"pkgname\")'. #>  #> Attaching package: ‘Biobase’ #> The following object is masked from ‘package:MatrixGenerics’: #>  #>     rowMedians #> The following objects are masked from ‘package:matrixStats’: #>  #>     anyMissing, rowMedians #>  #> Attaching package: ‘hermes’ #> The following object is masked from ‘package:stats’: #>  #>     filter object <- HermesData(summarized_experiment) result <- heatmap_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include CSS files from /inst/css/ package directory to application header — include_css_files","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"","code":"include_css_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"pattern (character) pattern files included","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_css_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include CSS files from /inst/css/ package directory to application header — include_css_files","text":"HTML code includes CSS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":null,"dir":"Reference","previous_headings":"","what":"Include JS files from /inst/js/ package directory to application header — include_js_files","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"system.file used access files packages, work devtools. Therefore, redefine method package needed. Thus, export method","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"","code":"include_js_files(pattern = \"*\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"pattern (character) pattern files included, passed system.file except (character) vector basename filenames excluded","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/include_js_files.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Include JS files from /inst/js/ package directory to application header — include_js_files","text":"HTML code includes JS files","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":null,"dir":"Reference","previous_headings":"","what":"Checking for Empty String — is_blank","title":"Checking for Empty String — is_blank","text":"predicate function helpful functions arguments yet initialized teal module.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(x)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Checking for Empty String — is_blank","text":"x object check.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Checking for Empty String — is_blank","text":"Flag whether x identical empty string, .e. \"\".","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/is_blank.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Checking for Empty String — is_blank","text":"","code":"is_blank(\"\") #> [1] TRUE is_blank(\" \") #> [1] FALSE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/module_arguments.html","id":null,"dir":"Reference","previous_headings":"","what":"Standard Module Arguments — module_arguments","title":"Standard Module Arguments — module_arguments","text":"documentation function lists conventional arguments hermes teal modules.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/module_arguments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Standard Module Arguments — module_arguments","text":"data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. label (string) menu item label module teal app. inputId (string) ID used call module input. adtte_name (string) name ADTTE dataset. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . reporter (Reporter) object pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. filter_panel_api (FilterPanelAPI) object describing actual filter panel API.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"multiple sample variables used given module, wrapper makes much easier specify server function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"multiSampleVarSpecServer(inputIds, original_data, ...)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"inputIds (character) multiple input IDs corresponding different sample variables specified UI function. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. ... additional arguments documented sampleVarSpecServer(), namely mandatory experiment_name optional categorical_only, num_levels label_modal_title. transformed_data assign_lists specified already specified internally .","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"List final transformed experiment_data reactive list vars contains selected sample variables reactives input ID.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/multiSampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Specification of Multiple Sample Variables — multiSampleVarSpecServer","text":"","code":"if (FALSE) { # In the server use: sample_var_specs <- multiSampleVarSpecServer(   inputIds = c(\"facet_var\", \"color_var\"),   experiment_name = reactive({     input$experiment_name   }),   original_data = ori_data # nolint Please update the <ori_data> ) # Then can extract the transformed data and selected variables later: experiment_data <- sample_var_specs$experiment_data() facet_var <- sample_var_specs$vars$facet_var() color_var <- sample_var_specs$vars$color_var() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":null,"dir":"Reference","previous_headings":"","what":"Random Time to Event Analysis Dataset — rADTTE","title":"Random Time to Event Analysis Dataset — rADTTE","text":"Random Time Event Analysis Dataset","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random Time to Event Analysis Dataset — rADTTE","text":"","code":"rADTTE"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Random Time to Event Analysis Dataset — rADTTE","text":"object class tbl_df (inherits tbl, data.frame) 2000 rows 67 columns.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/rADTTE.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Random Time to Event Analysis Dataset — rADTTE","text":"internal","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Input for Sample Variable Specification — sampleVarSpecInput","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"defines input sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(   inputId,   label_vars = \"Select sample variable\",   label_levels_button = \"Combine factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"inputId (string) ID used call module input. label_vars (string) label sample variable selection. label_levels_button (string) label levels combination button.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"UI part.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecInput.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Input for Sample Variable Specification — sampleVarSpecInput","text":"","code":"sampleVarSpecInput(\"my_vars\", label_vars = \"Select faceting variable\") #> <div class=\"row\"> #>   <div class=\"col-sm-8\"> #>     <label class=\"control-label\">Select faceting variable<\/label> #>   <\/div> #>   <div class=\"col-sm-4\"> #>     <button class=\"btn btn-default action-button pull-right list-genes\" id=\"my_vars-levels_button\" title=\"Combine factor levels\" type=\"button\"> #>       <span> #>         <i class=\"fas fa-table\" role=\"presentation\" aria-label=\"table icon\"><\/i> #>       <\/span> #>     <\/button> #>   <\/div> #> <\/div> #> <div class=\"custom-select-input\"> #>   <div> #>     <script> #>         $(function() { #>           $('#my_vars-sample_var').on('change', function(e) { #>             var select_concat = $(this).val().length ? $(this).val().join(', ') : 'NULL'; #>             $('#my_vars-sample_var_selected_text').html(select_concat); #>           }) #>         })<\/script> #>     <div> #>       <div id=\"my_vars-sample_var_input\" style=\"display: block;\"> #>         <div class=\"form-group shiny-input-container\"> #>           <label class=\"control-label shiny-label-null\" for=\"my_vars-sample_var\" id=\"my_vars-sample_var-label\"><\/label> #>           <select data-actions-box=\"false\" data-none-selected-text=\"- Nothing selected -\" data-max-options=\"1\" data-show-subtext=\"true\" data-live-search=\"false\" data-state-input=\"true\" id=\"my_vars-sample_var\" class=\"selectpicker form-control\" multiple=\"multiple\"><option value=\"\"><\/option><\/select> #>         <\/div> #>       <\/div> #>       <div id=\"my_vars-sample_var_fixed\" style=\"display: none;\"> #>         <label class=\"control-label\"><\/label> #>         <code id=\"my_vars-sample_var_selected_text\">NULL<\/code> #>       <\/div> #>     <\/div> #>   <\/div> #> <\/div>"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":null,"dir":"Reference","previous_headings":"","what":"Module Server for Sample Variable Specification — sampleVarSpecServer","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"defines server part sample variable specification.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"sampleVarSpecServer(   id,   experiment_name,   original_data,   transformed_data = original_data,   assign_lists = reactiveValues(),   num_levels = NULL,   categorical_only = !is.null(num_levels),   explicit_na = FALSE,   label_modal_title = \"Please click to group the original factor levels\" )"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"id (string) shiny module id. experiment_name (reactive string) name input experiment. original_data (reactive SummarizedExperiment) input experiment sample variables extracted via SummarizedExperiment::colData() eligible selection. transformed_data (reactive SummarizedExperiment) used multiple sample variables can selected app. case, pass pre-transformed data. assign_lists (reactivevalues) object share factor level groupings across multiple sample variables. num_levels (count NULL) required number levels combining original levels. NULL numbers levels allowed. categorical_only (flag) whether categorical variables selected . explicit_na (flag) whether colData original_data transformed hermes::h_df_factors_with_explicit_na processing. means also NA made explicit factor level counted num_levels. label_modal_title (string) title dialog asks text input.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"Reactive SummarizedExperiment::SummarizedExperiment can used input relevant hermes functions.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"atomic columns (e.g. DataFrame columns) colData completely missing (NA) shown selection. num_levels specified factor columns available.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/sampleVarSpecServer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Module Server for Sample Variable Specification — sampleVarSpecServer","text":"","code":"ui <- function(id,                data) {   ns <- NS(id)   mae <- data[[\"MAE\"]]()   experiment_name_choices <- names(mae)   teal.widgets::standard_layout(     encoding = div(       selectInput(ns(\"experiment_name\"), \"Select experiment\", experiment_name_choices),       sampleVarSpecInput(ns(\"facet_var\"), \"Select faceting variable\")     ),     output = plotOutput(ns(\"plot\"))   ) } server <- function(id,                    data) {   moduleServer(id, function(input, output, session) {     experiment_data <- reactive({       req(input$experiment_name)       mae <- data[[\"MAE\"]]()       object <- mae[[input$experiment_name]]       SummarizedExperiment::colData(object) <-         hermes::df_cols_to_factor(SummarizedExperiment::colData(object))       object     })     facet_var_spec <- sampleVarSpecServer(       \"facet_var\",       experiment_name = reactive({         input$experiment_name       }),       original_data = experiment_data     )     output$plot <- renderPlot({       experiment_data_final <- facet_var_spec$experiment_data()       facet_var <- facet_var_spec$sample_var()       hermes::draw_boxplot(         experiment_data_final,         assay_name = \"counts\",         genes = hermes::gene_spec(hermes::genes(experiment_data_final)[1]),         facet_var = facet_var       )     })   }) } my_app <- function() {   data <- teal_data(MAE = hermes::multi_assay_experiment)   app <- init(     data = data,     modules = modules(       module(         label = \"sampleVarSpec example\",         server = server,         ui = ui,         datanames = \"all\"       )     )   )   shinyApp(app$ui, app$server) } if (interactive()) {   my_app() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/teal.modules.hermes-package.html","id":null,"dir":"Reference","previous_headings":"","what":"teal.modules.hermes Package — teal.modules.hermes-package","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"teal.modules.hermes provides RNA-seq analysis modules add teal application.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/teal.modules.hermes-package.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"teal.modules.hermes Package — teal.modules.hermes-package","text":"Maintainer: Daniel Sabanés Bové daniel.sabanes_bove@roche.com Authors: Nikolas Burkoff Dinakar Kulkarni Konrad Pagacz Namrata Bhatia Dawid Kaledkowski Pawel Rucki Jeff Luong Stefanie Bienert Haocheng Li Lyndsee Midori Zhang contributors: Sorin Voicu [contributor] Benoit Falquet [contributor] Mahmoud Hallal [contributor] Tim Treis [contributor] F. Hoffmann-La Roche AG [copyright holder, funder]","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Barplot — tm_g_barplot","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"module provides interactive barplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"tm_g_barplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_barplot(id, data, mae_name, summary_funs, pre_output, post_output)  srv_g_barplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs )  sample_tm_g_barplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"ui_g_barplot(): sets user interface. srv_g_barplot(): sets server reactive graph. sample_tm_g_barplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_barplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Barplot — tm_g_barplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_barplot(       label = \"barplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-30 21:22:02.9875 pid:1284 token:[] teal.modules.hermes Initializing tm_g_barplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_barplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"module provides interactive boxplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"tm_g_boxplot(   label,   mae_name,   exclude_assays = character(),   summary_funs = list(None = NULL, Mean = colMeans, Median = matrixStats::colMedians, Max     = matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_boxplot(id, data, mae_name, summary_funs, pre_output, post_output)  srv_g_boxplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs )  sample_tm_g_boxplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"ui_g_boxplot(): sets user interface. srv_g_boxplot(): sets server reactive graph. sample_tm_g_boxplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_boxplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Boxplot — tm_g_boxplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_boxplot(       label = \"boxplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-30 21:22:03.3175 pid:1284 token:[] teal.modules.hermes Initializing tm_g_boxplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_boxplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Survival Forest Plot — tm_g_forest_tte","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"module provides interactive survival forest plot.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"tm_g_forest_tte(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL,   plot_height = c(600L, 200L, 2000L),   plot_width = c(1360L, 500L, 2000L) )  ui_g_forest_tte(   id,   data,   adtte_name,   mae_name,   summary_funs,   pre_output,   post_output )  srv_g_forest_tte(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   exclude_assays,   summary_funs,   plot_height,   plot_width )  sample_tm_g_forest_tte()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). plot_height (list) list integers set default, minimum, maximum plot height. plot_width (list) list integers set default, minimum, maximum plot width. id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"ui_g_forest_tte(): sets user interface. srv_g_forest_tte(): sets server reactive graph. sample_tm_g_forest_tte(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_forest_tte.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Survival Forest Plot — tm_g_forest_tte","text":"","code":"data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")  app <- init(   data = data,   modules = modules(     tm_g_forest_tte(       label = \"forestplot\",       adtte_name = \"ADTTE\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-30 21:22:03.6290 pid:1284 token:[] teal.modules.hermes Initializing tm_g_forest_tte if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_forest_tte() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for Kaplan-Meier Plot — tm_g_km","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"teal module produces grid style Kaplan-Meier plot data ADaM structure.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"tm_g_km(   label,   adtte_name,   mae_name,   adtte_vars = list(aval = \"AVAL\", is_event = \"is_event\", paramcd = \"PARAMCD\", usubjid =     \"USUBJID\", avalu = \"AVALU\"),   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_km(id, data, adtte_name, mae_name, summary_funs, pre_output, post_output)  srv_g_km(   id,   data,   filter_panel_api,   reporter,   adtte_name,   mae_name,   adtte_vars,   summary_funs,   exclude_assays )  sample_tm_g_km()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"label (string) menu item label module teal app. adtte_name (string) name ADTTE dataset. mae_name (string) name MAE data used teal module. adtte_vars (named list string) names variables use ADTTE dataset. comprise elements: aval: numeric time--event variable. avalu: variable holding unit aval. is_event: logical event variable. needs TRUE observed event, FALSE time censored without observed event. paramcd: character factor parameter code variable, defining type time--event selection module. usubjid: subject ID variable. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"ui_g_km(): sets user interface. srv_g_km(): sets user interface. sample_tm_g_km(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_km.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for Kaplan-Meier Plot — tm_g_km","text":"","code":"data <- teal_data() data <- within(data, {   ADTTE <- teal.modules.hermes::rADTTE %>%     dplyr::mutate(is_event = .data$CNSR == 0)   MAE <- hermes::multi_assay_experiment }) datanames <- c(\"ADTTE\", \"MAE\") datanames(data) <- datanames join_keys(data)[\"ADTTE\", \"ADTTE\"] <- c(\"STUDYID\", \"USUBJID\", \"PARAMCD\")   modules <- modules(   tm_g_km(     label = \"kaplan-meier\",     adtte_name = \"ADTTE\",     mae_name = \"MAE\"   ) ) #> [INFO] 2023-11-30 21:22:04.2513 pid:1284 token:[] teal.modules.hermes Initializing tm_g_km  app <- init(   data = data,   modules = modules )  if (interactive()) {   shinyApp(ui = app$ui, server = app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_km() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for PCA Analysis — tm_g_pca","title":"Teal Module for PCA Analysis — tm_g_pca","text":"module provides interactive principal components plot interactive heatmap correlation principal components sample variables.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"tm_g_pca(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL )  ui_g_pca(id, data, mae_name, pre_output, post_output)  srv_g_pca(id, data, filter_panel_api, reporter, mae_name, exclude_assays)  sample_tm_g_pca()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for PCA Analysis — tm_g_pca","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for PCA Analysis — tm_g_pca","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for PCA Analysis — tm_g_pca","text":"ui_g_pca(): sets user interface. srv_g_pca(): sets server reactive graph. sample_tm_g_pca(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for PCA Analysis — tm_g_pca","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_pca(       label = \"PCA plot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-30 21:22:04.5832 pid:1284 token:[] teal.modules.hermes Initializing tm_g_pca if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_pca() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Quality Control — tm_g_quality","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"module adds quality flags, filters genes /samples, normalizes AnyHermesData objects provides interactive plots RNA-seq gene expression quality control.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"tm_g_quality(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL )  ui_g_quality(id, data, mae_name, pre_output, post_output)  srv_g_quality(id, data, filter_panel_api, reporter, mae_name, exclude_assays)  sample_tm_g_quality()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"ui_g_quality(): sets user interface. srv_g_quality(): sets server reactive graphs. sample_tm_g_quality(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_quality.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Quality Control — tm_g_quality","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_quality(       label = \"Quality Control\",       mae_name = \"MAE\"     )   ) ) if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_quality() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"module provides interactive scatterplot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"tm_g_scatterplot(   label,   mae_name,   exclude_assays = \"counts\",   summary_funs = list(Mean = colMeans, Median = matrixStats::colMedians, Max =     matrixStats::colMaxs),   pre_output = NULL,   post_output = NULL )  ui_g_scatterplot(id, data, mae_name, summary_funs, pre_output, post_output)  srv_g_scatterplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays,   summary_funs )  sample_tm_g_scatterplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. summary_funs (named list functions NULL) functions can used gene signatures. modules support also multiple genes without summary, NULL can included summarize genes provide . pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"ui_g_scatterplot(): sets user interface. srv_g_scatterplot(): sets server reactive graph. sample_tm_g_scatterplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_scatterplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Scatterplot — tm_g_scatterplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_scatterplot(       label = \"scatterplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-30 21:22:05.1668 pid:1284 token:[] teal.modules.hermes Initializing tm_g_scatterplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_scatterplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":null,"dir":"Reference","previous_headings":"","what":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"module provides interactive volcano plot RNA-seq gene expression analysis.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"tm_g_volcanoplot(   label,   mae_name,   exclude_assays = character(),   pre_output = NULL,   post_output = NULL )  ui_g_volcanoplot(id, data, mae_name, pre_output, post_output)  srv_g_volcanoplot(   id,   data,   filter_panel_api,   reporter,   mae_name,   exclude_assays )  sample_tm_g_volcanoplot()"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"label (string) menu item label module teal app. mae_name (string) name MAE data used teal module. exclude_assays (character) names assays included choices teal module. pre_output (shiny.tag NULL) placed output put output context (example title). post_output (shiny.tag NULL) placed output put output context (example shiny::helpText() elements can useful). id (string) shiny module id. data (tdata)tdata object automatically passed UI server functions, holding data sets provided app initialization. filter_panel_api (FilterPanelAPI) object describing actual filter panel API. reporter (Reporter) object","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"Shiny module used teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"ui_g_volcanoplot(): sets user interface. srv_g_volcanoplot(): sets server reactive graph. sample_tm_g_volcanoplot(): sample module function.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/tm_g_volcanoplot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Teal Module for RNA-seq Volcano Plot — tm_g_volcanoplot","text":"","code":"data <- teal_data(MAE = hermes::multi_assay_experiment) app <- init(   data = data,   modules = modules(     tm_g_volcanoplot(       label = \"volcanoplot\",       mae_name = \"MAE\"     )   ) ) #> [INFO] 2023-11-30 21:22:05.4534 pid:1284 token:[] teal.modules.hermes Initializing tm_g_volcanoplot if (interactive()) {   shinyApp(app$ui, app$server) }  # Alternatively you can run the sample module with this function call: if (interactive()) {   sample_tm_g_volcanoplot() }"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Most Expressed Genes Plot — top_gene_plot","title":"Most Expressed Genes Plot — top_gene_plot","text":"function plots expressed genes.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"top_gene_plot(object, assay_name)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Most Expressed Genes Plot — top_gene_plot","text":"object (AnyHermesData) contains RNA-seq values one experiment. assay_name (string) assay define groups.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Most Expressed Genes Plot — top_gene_plot","text":"Plot displayed teal app.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/top_gene_plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Most Expressed Genes Plot — top_gene_plot","text":"","code":"library(hermes) object <- HermesData(summarized_experiment) result <- top_gene_plot(object, assay_name = \"counts\")"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_gene_spec.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Gene Specification — validate_gene_spec","title":"Validation of Gene Specification — validate_gene_spec","text":"validation function checks given hermes::GeneSpec least one gene selected genes included possible choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_gene_spec.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Gene Specification — validate_gene_spec","text":"","code":"validate_gene_spec(gene_spec, gene_choices)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_gene_spec.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Gene Specification — validate_gene_spec","text":"gene_spec (GeneSpec) gene specification. gene_choices (character) possible gene choices.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_n_levels.html","id":null,"dir":"Reference","previous_headings":"","what":"Validation of Number of Levels — validate_n_levels","title":"Validation of Number of Levels — validate_n_levels","text":"validation function checks given vector x factor specified number levels.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_n_levels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Validation of Number of Levels — validate_n_levels","text":"","code":"validate_n_levels(x, name, n_levels)"},{"path":"https://insightsengineering.github.io/teal.modules.hermes/reference/validate_n_levels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Validation of Number of Levels — validate_n_levels","text":"x (factor) factor validate. name (string) name x app. n_levels (count) required number factor levels x.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-5-9007","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.5.9007","text":"Added placeholders assaySpec, adtteSpec geneSpec inputs option selected. Disabled select input assaySpec adtteSpec options available.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"enhancements-0-1-5-9007","dir":"Changelog","previous_headings":"","what":"Enhancements","title":"teal.modules.hermes 0.1.5.9007","text":"Updated documentation vignettes new way specifying data teal::init(). data argument accepts teal_data object.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"bug-fixes-0-1-5","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.5","text":"Filtering data filter panel now correctly triggers sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"breaking-changes-0-1-5","dir":"Changelog","previous_headings":"","what":"Breaking changes","title":"teal.modules.hermes 0.1.5","text":"Replaced datasets argument containing FilteredData new arguments data (tdata object) filter_panel_api (FilterPanelAPI).","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-5","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.5","text":"Removed scda dependencies. Migrate shinytest2.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-014","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.4","title":"teal.modules.hermes 0.1.4","text":"Added teal.reporter functionality modules. Add installation instruction","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-013","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.3","title":"teal.modules.hermes 0.1.3","text":"Improve selection sample variables forest module (tm_g_forest_tte) categorical variables can selected first place.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-3","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.3","text":"Added template pkgdown site. Updated package authors. Added option categorical_only sampleVarSpec server module, allows show categorical sample variables selection.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-012","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.2","title":"teal.modules.hermes 0.1.2","text":"Rewrote modules use moduleServer updated call plot_with_settings_srv changes teal.devel. Replaced calls teal::root_modules teal::modules following deprecation teal::root_modules. Added basic logging modules. Fixed geneSpecInput hermes app doesn’t fail anymore (chrome) experiment genes.","code":""},{"path":[]},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"bug-fixes-0-1-1","dir":"Changelog","previous_headings":"","what":"Bug Fixes","title":"teal.modules.hermes 0.1.1","text":"Updated legend PCA plot. Gene selection thousand genes longer hangs application. achieved different selection input corresponding geneSpec shiny module. atomic columns colData least one value can now selected sampleVarSpecModule.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"miscellaneous-0-1-1","dir":"Changelog","previous_headings":"","what":"Miscellaneous","title":"teal.modules.hermes 0.1.1","text":"Updated R version requirement >= 3.6. Updated sampleVarSpec geneSpec modules new icons remove warnings using shiny version >= 1.7. Removed dependencies deprecated packages utils.nest test.nest.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"tealmoduleshermes-010","dir":"Changelog","previous_headings":"","what":"teal.modules.hermes 0.1.0","title":"teal.modules.hermes 0.1.0","text":"First release teal.modules.hermes package, contains teal modules RNA-seq analysis using hermes package. New users first begin reading README.md teal.modules.hermes package become familiar.","code":""},{"path":"https://insightsengineering.github.io/teal.modules.hermes/news/index.html","id":"new-features-0-1-0","dir":"Changelog","previous_headings":"","what":"New Features","title":"teal.modules.hermes 0.1.0","text":"tm_g_barplot barplot module RNA-seq gene expression analysis. tm_g_boxplot boxplot module RNA-seq gene expression analysis. tm_g_forest_tte survival forest plot module analyze RNA-seq gene expression data together survival data. tm_g_km Kaplan-Meier plot module analyze RNA-seq gene expression data together survival data. tm_g_pca principal components analysis plot module RNA-seq gene expression analysis. tm_g_quality quality control module RNA-seq gene expression data. tm_g_scatterplot scatterplot module RNA-seq gene expression analysis. tm_g_volcanoplot differential gene expression analysis module.","code":""}]