WGCNA.qmd

cox-labs · Nov 28, 2024 · c47dbd6 · c47dbd6
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diff --git a/WGCNA.qmd b/WGCNA.qmd
@@ -31,18 +31,22 @@ This package is provided through the R-language integration into Perseus and the
   * Check that R is installed correctly by opening `cmd.exe` from the start menu and entering `R` An R session should start.
   * Inside the running R session, install the [WGCNA](https://cran.r-project.org/web/packages/WGCNA/index.html) and [PerseusR](https://github.com/jdrudolph/PerseusR) libraries by entering/pasting the following code **line-by-line**. 
   When prompted for local install, type ‘yes’ twice and select a close-by server for the package download. 
-```{r}
-# | eval: false
+
+```
+
 install.packages("BiocManager")
 BiocManager::install(c("WGCNA", "devtools"))
 library(devtools)
 install_github('jdrudolph/PerseusR')
+
 ```
   * You should now be able to load the `WGCNA` and `PerseusR` libraries by entering the following code. Upon loading, `WGCNA` will print some output, while `PerseusR` will not print any.
-```{r}
-# | eval: false
+
+```
+
 library(WGCNA)
 library(PerseusR)
+
 ```
 
 You are now ready to perform co-expression analysis from within Perseus.

diff --git a/docs/WGCNA.html b/docs/WGCNA.html
@@ -2,12 +2,12 @@
 <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
 
 <meta charset="utf-8">
-<meta name="generator" content="quarto-1.4.315">
+<meta name="generator" content="quarto-1.5.57">
 
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 <meta name="author" content="Cox Lab">
-<meta name="dcterms.date" content="2023-11-15">
+<meta name="dcterms.date" content="2024-11-28">
 
 <title>WGCNA</title>
 <style>
@@ -22,40 +22,6 @@
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-    border: none; display: inline-block;
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-    -khtml-user-select: none; -moz-user-select: none;
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-pre.numberSource { margin-left: 3em;  padding-left: 4px; }
-div.sourceCode
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-}
 </style>
 
 
@@ -81,12 +47,13 @@
   "collapse-after": 3,
   "panel-placement": "end",
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-  "limit": 20,
+  "limit": 50,
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+  "show-item-context": false,
   "language": {
     "search-no-results-text": "No results",
     "search-matching-documents-text": "matching documents",
@@ -95,6 +62,7 @@
     "search-more-match-text": "more match in this document",
     "search-more-matches-text": "more matches in this document",
     "search-clear-button-title": "Clear",
+    "search-text-placeholder": "",
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@@ -109,15 +77,15 @@
 
 <div id="quarto-search-results"></div>
   <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
+    <nav class="navbar navbar-expand-lg " data-bs-theme="dark">
       <div class="navbar-container container-fluid">
       <div class="navbar-brand-container mx-auto">
     <a href="./index.html" class="navbar-brand navbar-brand-logo">
     <img src="./Figures/coxlab_logo2.png" alt="" class="navbar-logo">
     </a>
   </div>
             <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
+          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" role="menu" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
   <span class="navbar-toggler-icon"></span>
 </button>
           <div class="collapse navbar-collapse" id="navbarCollapse">
@@ -162,7 +130,7 @@
   </li>  
 </ul>
           </div> <!-- /navcollapse -->
-          <div class="quarto-navbar-tools">
+            <div class="quarto-navbar-tools">
 </div>
       </div> <!-- /container-fluid -->
     </nav>
@@ -204,7 +172,7 @@ <h1 class="title">WGCNA</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">November 15, 2023</p>
+      <p class="date">November 28, 2024</p>
     </div>
   </div>
 
@@ -215,6 +183,7 @@ <h1 class="title">WGCNA</h1>
 
 </header>
 
+
 <section id="weighted-gene-co-expression-network-analysis" class="level2" data-number="1">
 <h2 data-number="1" class="anchored" data-anchor-id="weighted-gene-co-expression-network-analysis"><span class="header-section-number">1</span> Weighted Gene Co-expression Network Analysis</h2>
 <p>This package is provided through the R-language integration into Perseus and therefore requires R as well as the package itself to be installed in order to be used. Visit the <a href="https://github.com/jdrudolph/PluginInterop">PluginInterop</a> and <a href="https://github.com/jdrudolph/PerseusR">PerseusR</a> for additional technical information on the integration of R and Perseus.</p>
@@ -231,21 +200,19 @@ <h2 data-number="2" class="anchored" data-anchor-id="installation"><span class="
 <li>Check that R is installed correctly by opening <code>cmd.exe</code> from the start menu and entering <code>R</code> An R session should start.</li>
 <li>Inside the running R session, install the <a href="https://cran.r-project.org/web/packages/WGCNA/index.html">WGCNA</a> and <a href="https://github.com/jdrudolph/PerseusR">PerseusR</a> libraries by entering/pasting the following code <strong>line-by-line</strong>. When prompted for local install, type ‘yes’ twice and select a close-by server for the package download.</li>
 </ul>
-<div class="cell">
-<div class="sourceCode cell-code" id="cb1"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="co"># | eval: false</span></span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">"BiocManager"</span>)</span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>BiocManager<span class="sc">::</span><span class="fu">install</span>(<span class="fu">c</span>(<span class="st">"WGCNA"</span>, <span class="st">"devtools"</span>))</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(devtools)</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="fu">install_github</span>(<span class="st">'jdrudolph/PerseusR'</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</div>
+<pre><code>
+install.packages("BiocManager")
+BiocManager::install(c("WGCNA", "devtools"))
+library(devtools)
+install_github('jdrudolph/PerseusR')
+</code></pre>
 <ul>
 <li>You should now be able to load the <code>WGCNA</code> and <code>PerseusR</code> libraries by entering the following code. Upon loading, <code>WGCNA</code> will print some output, while <code>PerseusR</code> will not print any.</li>
 </ul>
-<div class="cell">
-<div class="sourceCode cell-code" id="cb2"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># | eval: false</span></span>
-<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(WGCNA)</span>
-<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(PerseusR)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</div>
+<pre><code>
+library(WGCNA)
+library(PerseusR)
+</code></pre>
 <p>You are now ready to perform co-expression analysis from within Perseus.</p>
 </section>
 <section id="wgcna-functions" class="level2" data-number="3">
@@ -294,18 +261,7 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
     }
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+  const onCopySuccess = function(e) {
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     // don't keep focus
@@ -337,7 +293,47 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
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+    // For code content inside modals, clipBoardJS needs to be initialized with a container option
+    // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
+    const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
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@@ -372,7 +368,11 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
       try { href = new URL(href).hash; } catch {}
       const id = href.replace(/^#\/?/, "");
       const note = window.document.getElementById(id);
-      return note.innerHTML;
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   const xrefs = window.document.querySelectorAll('a.quarto-xref');
@@ -387,15 +387,28 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
       }
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@@ -404,7 +417,15 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
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         anchorLink.remove();
       }
-      return note.innerHTML;
+      if (window.Quarto?.typesetMath) {
+        window.Quarto.typesetMath(note);
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+      // TODO in 1.5, we should make sure this works without a callout special case
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+        return note.outerHTML;
+      } else {
+        return note.innerHTML;
+      }
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@@ -446,6 +467,29 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
             instance.show();
           });
         }
+      } else {
+        // See if we can fetch a full url (with no hash to target)
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+        .then(res => res.text())
+        .then(html => {
+          const parser = new DOMParser();
+          const htmlDoc = parser.parseFromString(html, "text/html");
+          const note = htmlDoc.querySelector('main.content');
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@@ -521,7 +565,6 @@ <h2 data-number="3" class="anchored" data-anchor-id="wgcna-functions"><span clas
     window.addEventListener(
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diff --git a/docs/ngsupload.html b/docs/ngsupload.html
@@ -454,7 +454,8 @@ <h1 data-number="7"><span class="header-section-number">7</span> Comparison with
   has_icon = TRUE,
   icon = "fa fa-save",
   self_contained = FALSE
-)</code></pre>
+)
+</code></pre>
 <!-- ==== Parameters specific for "Chromatin IP" experiment ====
 The most popular way to deal with Chromatin IP experiment is sequence relatively small part of a read - enough for unique alignment - and already in silico extend such read until expected length.
 {{ :user:activities:matrixupload:chipseqextend.png?500 |}}

diff --git a/ngsupload.qmd b/ngsupload.qmd
@@ -149,6 +149,7 @@ download_file(
   icon = "fa fa-save",
   self_contained = FALSE
 )
+
 ```
-Original file line number
+Diff line change
@@ Expand Up / @@ -149,6 +149,7 @@ download_file( @@
       icon = "fa fa-save",
       self_contained = FALSE
     )
     ```
@@ Expand Down @@