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            <h1 id="seo-header">WGCNA：官方教程学习之共识分析</h1>
            
            
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                <h2 id="数据清洗"><a href="#数据清洗" class="headerlink" title="数据清洗"></a>数据清洗</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>WGCNA<span class="hljs-punctuation">)</span>  <span class="hljs-comment">#加载WGCNA包</span><br>enableWGCNAThreads<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>  <span class="hljs-comment">#开启多线程</span><br>options<span class="hljs-punctuation">(</span>stringsAsFactors <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span>  <span class="hljs-comment">#避免某些错误匹配</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment">#Read in the female liver data set</span><br>femData <span class="hljs-operator">=</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;LiverFemale3600.csv&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Read in the male liver data set</span><br>maleData <span class="hljs-operator">=</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;LiverMale3600.csv&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># For easier labeling of plots, create a vector holding descriptive names of the two sets.</span><br>setLabels <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Female liver&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Male liver&quot;</span><span class="hljs-punctuation">)</span><br>shortLabels <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Female&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Male&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># We work with two sets:</span><br>nSets <span class="hljs-operator">=</span> <span class="hljs-number">2</span>;<br><span class="hljs-comment"># Form multi-set expression data: columns starting from 9 contain actual expression data.</span><br>multiExpr <span class="hljs-operator">=</span> vector<span class="hljs-punctuation">(</span>mode <span class="hljs-operator">=</span> <span class="hljs-string">&quot;list&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span> <span class="hljs-operator">=</span> nSets<span class="hljs-punctuation">)</span><br>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> as.data.frame<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>femData<span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> femData<span class="hljs-operator">$</span>substanceBXH;<br>rownames<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>femData<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span>;<br>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> as.data.frame<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>maleData<span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> maleData<span class="hljs-operator">$</span>substanceBXH;<br>rownames<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>maleData<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span>;<br><span class="hljs-comment"># Check that the data has the correct format for many functions operating on multiple sets:</span><br>exprSize <span class="hljs-operator">=</span> checkSets<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">)</span><br>exprSize<br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br></pre></td><td class="code"><pre><code class="hljs R">gsg <span class="hljs-operator">=</span> goodSamplesGenesMS<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span>;<br>gsg<span class="hljs-operator">$</span>allOK<br><span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>gsg<span class="hljs-operator">$</span>allOK<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-comment"># Print information about the removed genes:</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>gsg<span class="hljs-operator">$</span>goodGenes<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        printFlush<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Removing genes:&quot;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">!</span>gsg<span class="hljs-operator">$</span>goodGenes<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>collapse <span class="hljs-operator">=</span> <span class="hljs-string">&quot;, &quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>exprSize<span class="hljs-operator">$</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>gsg<span class="hljs-operator">$</span>goodSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            printFlush<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;In set&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;removing samples&quot;</span><span class="hljs-punctuation">,</span><br>            paste<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">!</span>gsg<span class="hljs-operator">$</span>goodSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&quot;, &quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><br>        <span class="hljs-comment"># Remove the offending genes and samples</span><br>        multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data <span class="hljs-operator">=</span> multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span>gsg<span class="hljs-operator">$</span>goodSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> gsg<span class="hljs-operator">$</span>goodGenes<span class="hljs-punctuation">]</span>;<br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-comment"># Update exprSize</span><br>    exprSize <span class="hljs-operator">=</span> checkSets<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br></pre></td><td class="code"><pre><code class="hljs R">sampleTrees <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    sampleTrees<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> hclust<span class="hljs-punctuation">(</span>dist<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;average&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    plot<span class="hljs-punctuation">(</span>sampleTrees<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> main <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Sample clustering on all genes in&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>        xlab<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> sub<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> cex <span class="hljs-operator">=</span> <span class="hljs-number">0.7</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Choose the &quot;base&quot; cut height for the female data set</span><br>baseHeight <span class="hljs-operator">=</span> <span class="hljs-number">16</span><br><span class="hljs-comment"># Adjust the cut height for the male data set for the number of samples</span><br>cutHeights <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> exprSize<span class="hljs-operator">$</span>nSamples<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-operator">/</span>exprSize<span class="hljs-operator">$</span>nSamples<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span>baseHeight<br><span class="hljs-comment"># Re-plot the dendrograms including the cut lines</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    plot<span class="hljs-punctuation">(</span>sampleTrees<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> main <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Sample clustering on all genes in&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>        xlab<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> sub<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> cex <span class="hljs-operator">=</span> <span class="hljs-number">0.7</span><span class="hljs-punctuation">)</span>;<br>    abline<span class="hljs-punctuation">(</span>h<span class="hljs-operator">=</span>cutHeights<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> <span class="hljs-string">&quot;red&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-comment"># Find clusters cut by the line</span><br>    labels <span class="hljs-operator">=</span> cutreeStatic<span class="hljs-punctuation">(</span>sampleTrees<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> cutHeight <span class="hljs-operator">=</span> cutHeights<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment"># Keep the largest one (labeled by the number 1)</span><br>    keep <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>labels<span class="hljs-operator">==</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data <span class="hljs-operator">=</span> multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br>collectGarbage<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Check the size of the leftover data</span><br>exprSize <span class="hljs-operator">=</span> checkSets<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">)</span><br>exprSize<br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs R">traitData <span class="hljs-operator">=</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;ClinicalTraits.csv&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># remove columns that hold information we do not need.</span><br>allTraits <span class="hljs-operator">=</span> traitData<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">31</span><span class="hljs-punctuation">,</span> <span class="hljs-number">16</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span>;<br>allTraits <span class="hljs-operator">=</span> allTraits<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <span class="hljs-number">11</span><span class="hljs-operator">:</span><span class="hljs-number">36</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span>;<br>Traits <span class="hljs-operator">=</span> vector<span class="hljs-punctuation">(</span>mode<span class="hljs-operator">=</span><span class="hljs-string">&quot;list&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span> <span class="hljs-operator">=</span> nSets<span class="hljs-punctuation">)</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    setSamples <span class="hljs-operator">=</span> rownames<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span>;<br>    traitRows <span class="hljs-operator">=</span> match<span class="hljs-punctuation">(</span>setSamples<span class="hljs-punctuation">,</span> allTraits<span class="hljs-operator">$</span>Mice<span class="hljs-punctuation">)</span>;<br>    Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> allTraits<span class="hljs-punctuation">[</span>traitRows<span class="hljs-punctuation">,</span> <span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>    rownames<span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> allTraits<span class="hljs-punctuation">[</span>traitRows<span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span>;<br><span class="hljs-punctuation">&#125;</span><br>collectGarbage<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br></code></pre></td></tr></table></figure>

<p>得到一个multiExpr，以列表的形式存储了所有的表达矩阵；一个Traits，以列表的形式存储了所有的性状矩阵</p>
<h2 id="构建共识网络模块"><a href="#构建共识网络模块" class="headerlink" title="构建共识网络模块"></a>构建共识网络模块</h2><h3 id="选择合适的β值"><a href="#选择合适的β值" class="headerlink" title="选择合适的β值"></a>选择合适的β值</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Choose a set of soft-thresholding powers</span><br>powers <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>seq<span class="hljs-punctuation">(</span><span class="hljs-number">4</span><span class="hljs-punctuation">,</span><span class="hljs-number">10</span><span class="hljs-punctuation">,</span>by<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> seq<span class="hljs-punctuation">(</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span><span class="hljs-number">20</span><span class="hljs-punctuation">,</span> by<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Initialize a list to hold the results of scale-free analysis</span><br>powerTables <span class="hljs-operator">=</span> vector<span class="hljs-punctuation">(</span>mode <span class="hljs-operator">=</span> <span class="hljs-string">&quot;list&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span> <span class="hljs-operator">=</span> nSets<span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Call the network topology analysis function for each set in turn</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> pickSoftThreshold<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> powerVector<span class="hljs-operator">=</span>powers<span class="hljs-punctuation">,</span><br>        verbose <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-punctuation">&#125;</span><br>collectGarbage<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Plot the results:</span><br>colors <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;black&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;red&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Will plot these columns of the returned scale free analysis tables</span><br>plotCols <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span><span class="hljs-number">7</span><span class="hljs-punctuation">)</span><br>colNames <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Scale Free Topology Model Fit&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Mean connectivity&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Median connectivity&quot;</span><span class="hljs-punctuation">,</span><br><span class="hljs-string">&quot;Max connectivity&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Get the minima and maxima of the plotted points</span><br>ylim <span class="hljs-operator">=</span> matrix<span class="hljs-punctuation">(</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> nrow <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">,</span> ncol <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>col <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>plotCols<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        ylim<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> col<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">min</span><span class="hljs-punctuation">(</span>ylim<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> plotCols<span class="hljs-punctuation">[</span>col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> na.rm <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span>;<br>        ylim<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> col<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">max</span><span class="hljs-punctuation">(</span>ylim<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> plotCols<span class="hljs-punctuation">[</span>col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> na.rm <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span>;<br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br><span class="hljs-comment"># Plot the quantities in the chosen columns vs. the soft thresholding power</span><br>cex1 <span class="hljs-operator">=</span> <span class="hljs-number">0.7</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>col <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>plotCols<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>set<span class="hljs-operator">==</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        plot<span class="hljs-punctuation">(</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-operator">-</span><span class="hljs-built_in">sign</span><span class="hljs-punctuation">(</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>        xlab<span class="hljs-operator">=</span><span class="hljs-string">&quot;Soft Threshold (power)&quot;</span><span class="hljs-punctuation">,</span>ylab<span class="hljs-operator">=</span>colNames<span class="hljs-punctuation">[</span>col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>type<span class="hljs-operator">=</span><span class="hljs-string">&quot;n&quot;</span><span class="hljs-punctuation">,</span> ylim <span class="hljs-operator">=</span> ylim<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>        main <span class="hljs-operator">=</span> colNames<span class="hljs-punctuation">[</span>col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>        addGrid<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>col<span class="hljs-operator">==</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        text<span class="hljs-punctuation">(</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-operator">-</span><span class="hljs-built_in">sign</span><span class="hljs-punctuation">(</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-operator">*</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>        labels<span class="hljs-operator">=</span>powers<span class="hljs-punctuation">,</span>cex<span class="hljs-operator">=</span>cex1<span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span>colors<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>    <span class="hljs-punctuation">&#125;</span> <span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        text<span class="hljs-punctuation">(</span>powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> powerTables<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>plotCols<span class="hljs-punctuation">[</span>col<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>        labels<span class="hljs-operator">=</span>powers<span class="hljs-punctuation">,</span>cex<span class="hljs-operator">=</span>cex1<span class="hljs-punctuation">,</span>col<span class="hljs-operator">=</span>colors<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>col<span class="hljs-operator">==</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        legend<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;bottomright&quot;</span><span class="hljs-punctuation">,</span> legend <span class="hljs-operator">=</span> setLabels<span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> colors<span class="hljs-punctuation">,</span> pch <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span> ;<br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        legend<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;topright&quot;</span><span class="hljs-punctuation">,</span> legend <span class="hljs-operator">=</span> setLabels<span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> colors<span class="hljs-punctuation">,</span> pch <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span> ;<br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h3 id="计算邻接矩阵"><a href="#计算邻接矩阵" class="headerlink" title="计算邻接矩阵"></a>计算邻接矩阵</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs R">softPower <span class="hljs-operator">=</span> <span class="hljs-number">7</span>;<br><span class="hljs-comment"># Initialize an appropriate array to hold the adjacencies</span><br>nGenes <span class="hljs-operator">=</span> exprSize<span class="hljs-operator">$</span>nGenes;<br>nSamples <span class="hljs-operator">=</span> exprSize<span class="hljs-operator">$</span>nSamples;<br>adjacencies <span class="hljs-operator">=</span> array<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">dim</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>nSets<span class="hljs-punctuation">,</span> nGenes<span class="hljs-punctuation">,</span> nGenes<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Calculate adjacencies in each individual data set</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    adjacencies<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">abs</span><span class="hljs-punctuation">(</span>bicor<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> use <span class="hljs-operator">=</span> <span class="hljs-string">&quot;p&quot;</span><span class="hljs-punctuation">,</span> maxPOutliers <span class="hljs-operator">=</span> <span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-operator">^</span>softPower;<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h3 id="计算拓扑重叠矩阵"><a href="#计算拓扑重叠矩阵" class="headerlink" title="计算拓扑重叠矩阵"></a>计算拓扑重叠矩阵</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br></pre></td><td class="code"><pre><code class="hljs R">TOM <span class="hljs-operator">=</span> array<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">dim</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>nSets<span class="hljs-punctuation">,</span> nGenes<span class="hljs-punctuation">,</span> nGenes<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Calculate TOMs in each individual data set</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    TOM<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> TOMsimilarity<span class="hljs-punctuation">(</span>adjacencies<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h3 id="缩放拓扑重叠矩阵保证可比性"><a href="#缩放拓扑重叠矩阵保证可比性" class="headerlink" title="缩放拓扑重叠矩阵保证可比性"></a>缩放拓扑重叠矩阵保证可比性</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Define the reference percentile</span><br>scaleP <span class="hljs-operator">=</span> <span class="hljs-number">0.95</span><br><span class="hljs-comment"># Set RNG seed for reproducibility of sampling</span><br>set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">12345</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Sample sufficiently large number of TOM entries</span><br>nSamples <span class="hljs-operator">=</span> <span class="hljs-built_in">as.integer</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">/</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">-</span>scaleP<span class="hljs-punctuation">)</span> <span class="hljs-operator">*</span> <span class="hljs-number">1000</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Choose the sampled TOM entries</span><br>scaleSample <span class="hljs-operator">=</span> sample<span class="hljs-punctuation">(</span>nGenes<span class="hljs-operator">*</span><span class="hljs-punctuation">(</span>nGenes<span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-operator">/</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> size <span class="hljs-operator">=</span> nSamples<span class="hljs-punctuation">)</span><br>TOMScalingSamples <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># These are TOM values at reference percentile</span><br>scaleQuant <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> nSets<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Scaling powers to equalize reference TOM values</span><br>scalePowers <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> nSets<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Loop over sets</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-comment"># Select the sampled TOM entries</span><br>    TOMScalingSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> as.dist<span class="hljs-punctuation">(</span>TOM<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>scaleSample<span class="hljs-punctuation">]</span><br>    <span class="hljs-comment"># Calculate the 95th percentile</span><br>    scaleQuant<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> quantile<span class="hljs-punctuation">(</span>TOMScalingSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>    probs <span class="hljs-operator">=</span> scaleP<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-number">8</span><span class="hljs-punctuation">)</span>;<br>    <span class="hljs-comment"># Scale the male TOM</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>set<span class="hljs-operator">&gt;</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        scalePowers<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span>scaleQuant<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-operator">/</span><span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span>scaleQuant<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>        TOM<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> TOM<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-operator">^</span>scalePowers<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span>;<br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># For plotting, also scale the sampled TOM entries</span><br>scaledTOMSamples <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scaledTOMSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> TOMScalingSamples<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">^</span>scalePowers<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br><span class="hljs-comment"># qq plot of the unscaled samples</span><br>qqUnscaled <span class="hljs-operator">=</span> qqplot<span class="hljs-punctuation">(</span>TOMScalingSamples<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> TOMScalingSamples<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> plot.it <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> cex <span class="hljs-operator">=</span> <span class="hljs-number">0.6</span><span class="hljs-punctuation">,</span><br>    xlab <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;TOM in&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ylab <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;TOM in&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    main <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Q-Q plot of TOM&quot;</span><span class="hljs-punctuation">,</span> pch <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># qq plot of the scaled samples</span><br>qqScaled <span class="hljs-operator">=</span> qqplot<span class="hljs-punctuation">(</span>scaledTOMSamples<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> scaledTOMSamples<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> plot.it <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>points<span class="hljs-punctuation">(</span>qqScaled<span class="hljs-operator">$</span>x<span class="hljs-punctuation">,</span> qqScaled<span class="hljs-operator">$</span>y<span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> <span class="hljs-string">&quot;red&quot;</span><span class="hljs-punctuation">,</span> cex <span class="hljs-operator">=</span> <span class="hljs-number">0.6</span><span class="hljs-punctuation">,</span> pch <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span>;<br>abline<span class="hljs-punctuation">(</span>a<span class="hljs-operator">=</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> b<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> <span class="hljs-string">&quot;blue&quot;</span><span class="hljs-punctuation">)</span><br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;topleft&quot;</span><span class="hljs-punctuation">,</span> legend <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Unscaled TOM&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Scaled TOM&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> pch <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;black&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;red&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="计算共识拓扑重叠矩阵"><a href="#计算共识拓扑重叠矩阵" class="headerlink" title="计算共识拓扑重叠矩阵"></a>计算共识拓扑重叠矩阵</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs R">consensusTOM <span class="hljs-operator">=</span> pmin<span class="hljs-punctuation">(</span>TOM<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> TOM<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="聚类并鉴定网络模块"><a href="#聚类并鉴定网络模块" class="headerlink" title="聚类并鉴定网络模块"></a>聚类并鉴定网络模块</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Clustering</span><br>consTree <span class="hljs-operator">=</span> hclust<span class="hljs-punctuation">(</span>as.dist<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">-</span>consensusTOM<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;average&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># We like large modules, so we set the minimum module size relatively high:</span><br>minModuleSize <span class="hljs-operator">=</span> <span class="hljs-number">30</span>;<br><span class="hljs-comment"># Module identification using dynamic tree cut:</span><br>unmergedLabels <span class="hljs-operator">=</span> cutreeDynamic<span class="hljs-punctuation">(</span>dendro <span class="hljs-operator">=</span> consTree<span class="hljs-punctuation">,</span> distM <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">-</span>consensusTOM<span class="hljs-punctuation">,</span><br>deepSplit <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">,</span> cutHeight <span class="hljs-operator">=</span> <span class="hljs-number">0.995</span><span class="hljs-punctuation">,</span><br>minClusterSize <span class="hljs-operator">=</span> minModuleSize<span class="hljs-punctuation">,</span><br>pamRespectsDendro <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span> <span class="hljs-punctuation">)</span>;<br>unmergedColors <span class="hljs-operator">=</span> labels2colors<span class="hljs-punctuation">(</span>unmergedLabels<span class="hljs-punctuation">)</span><br>plotDendroAndColors<span class="hljs-punctuation">(</span>consTree<span class="hljs-punctuation">,</span> unmergedColors<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Dynamic Tree Cut&quot;</span><span class="hljs-punctuation">,</span><br>    dendroLabels <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> hang <span class="hljs-operator">=</span> <span class="hljs-number">0.03</span><span class="hljs-punctuation">,</span><br>    addGuide <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> guideHang <span class="hljs-operator">=</span> <span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="合并相似矩阵"><a href="#合并相似矩阵" class="headerlink" title="合并相似矩阵"></a>合并相似矩阵</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Calculate module eigengenes</span><br>unmergedMEs <span class="hljs-operator">=</span> multiSetMEs<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">,</span> colors <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> universalColors <span class="hljs-operator">=</span> unmergedColors<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Calculate consensus dissimilarity of consensus module eigengenes</span><br>consMEDiss <span class="hljs-operator">=</span> consensusMEDissimilarity<span class="hljs-punctuation">(</span>unmergedMEs<span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Cluster consensus modules</span><br>consMETree <span class="hljs-operator">=</span> hclust<span class="hljs-punctuation">(</span>as.dist<span class="hljs-punctuation">(</span>consMEDiss<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;average&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Plot the result</span><br>par<span class="hljs-punctuation">(</span>mfrow <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>consMETree<span class="hljs-punctuation">,</span> main <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Consensus clustering of consensus module eigengenes&quot;</span><span class="hljs-punctuation">,</span><br>    xlab <span class="hljs-operator">=</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> sub <span class="hljs-operator">=</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span><br>abline<span class="hljs-punctuation">(</span>h<span class="hljs-operator">=</span><span class="hljs-number">0.25</span><span class="hljs-punctuation">,</span> col <span class="hljs-operator">=</span> <span class="hljs-string">&quot;red&quot;</span><span class="hljs-punctuation">)</span><br>merge <span class="hljs-operator">=</span> mergeCloseModules<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">,</span> unmergedLabels<span class="hljs-punctuation">,</span> cutHeight <span class="hljs-operator">=</span> <span class="hljs-number">0.25</span><span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Numeric module labels</span><br>moduleLabels <span class="hljs-operator">=</span> merge<span class="hljs-operator">$</span>colors;<br><span class="hljs-comment"># Convert labels to colors</span><br>moduleColors <span class="hljs-operator">=</span> labels2colors<span class="hljs-punctuation">(</span>moduleLabels<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Eigengenes of the new merged modules:</span><br>consMEs <span class="hljs-operator">=</span> merge<span class="hljs-operator">$</span>newMEs<br>plotDendroAndColors<span class="hljs-punctuation">(</span>consTree<span class="hljs-punctuation">,</span> cbind<span class="hljs-punctuation">(</span>unmergedColors<span class="hljs-punctuation">,</span> moduleColors<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Unmerged&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Merged&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    dendroLabels <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> hang <span class="hljs-operator">=</span> <span class="hljs-number">0.03</span><span class="hljs-punctuation">,</span><br>    addGuide <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> guideHang <span class="hljs-operator">=</span> <span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="关联共识网络模块与普通网络模块"><a href="#关联共识网络模块与普通网络模块" class="headerlink" title="关联共识网络模块与普通网络模块"></a>关联共识网络模块与普通网络模块</h2><p><a target="_blank" rel="noopener" href="https://limour.top/1929.html">WGCNA：官方教程学习之网络分析</a>中获得了普通网络模块，将其导出</p>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Rename variables to avoid conflicts</span><br>femaleLabels <span class="hljs-operator">=</span> moduleLabels;<br>femaleColors <span class="hljs-operator">=</span> moduleColors;<br>femaleTree <span class="hljs-operator">=</span> geneTree;<br>femaleMEs <span class="hljs-operator">=</span> orderMEs<span class="hljs-punctuation">(</span>MEs<span class="hljs-punctuation">,</span> greyName <span class="hljs-operator">=</span> <span class="hljs-string">&quot;ME0&quot;</span><span class="hljs-punctuation">)</span>;<br>save<span class="hljs-punctuation">(</span>femaleMEs<span class="hljs-punctuation">,</span> femaleLabels<span class="hljs-punctuation">,</span> femaleColors<span class="hljs-punctuation">,</span> femaleTree<span class="hljs-punctuation">,</span><br>    file <span class="hljs-operator">=</span> <span class="hljs-string">&quot;FemaleLiver-02-networkConstruction.RData&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs R">lnames <span class="hljs-operator">=</span> load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;FemaleLiver-02-networkConstruction.RData&#x27;</span><span class="hljs-punctuation">)</span><br>lnames<br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Isolate the module labels in the order they appear in ordered module eigengenes</span><br>femModuleLabels <span class="hljs-operator">=</span> substring<span class="hljs-punctuation">(</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>femaleMEs<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br>consModuleLabels <span class="hljs-operator">=</span> substring<span class="hljs-punctuation">(</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>consMEs<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Convert the numeric module labels to color labels</span><br>femModules <span class="hljs-operator">=</span> femModuleLabels<br>consModules <span class="hljs-operator">=</span> labels2colors<span class="hljs-punctuation">(</span><span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>consModuleLabels<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Numbers of female and consensus modules</span><br>nFemMods <span class="hljs-operator">=</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>femModules<span class="hljs-punctuation">)</span><br>nConsMods <span class="hljs-operator">=</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>consModules<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Initialize tables of p-values and of the corresponding counts</span><br>pTable <span class="hljs-operator">=</span> matrix<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> nrow <span class="hljs-operator">=</span> nFemMods<span class="hljs-punctuation">,</span> ncol <span class="hljs-operator">=</span> nConsMods<span class="hljs-punctuation">)</span>;<br>CountTbl <span class="hljs-operator">=</span> matrix<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> nrow <span class="hljs-operator">=</span> nFemMods<span class="hljs-punctuation">,</span> ncol <span class="hljs-operator">=</span> nConsMods<span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Execute all pairwaise comparisons</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>fmod <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nFemMods<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>cmod <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nConsMods<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        femMembers <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>femaleColors <span class="hljs-operator">==</span> femModules<span class="hljs-punctuation">[</span>fmod<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>        consMembers <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>moduleColors <span class="hljs-operator">==</span> consModules<span class="hljs-punctuation">[</span>cmod<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>        pTable<span class="hljs-punctuation">[</span>fmod<span class="hljs-punctuation">,</span> cmod<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-operator">-</span>log10<span class="hljs-punctuation">(</span>fisher.test<span class="hljs-punctuation">(</span>femMembers<span class="hljs-punctuation">,</span> consMembers<span class="hljs-punctuation">,</span> alternative <span class="hljs-operator">=</span> <span class="hljs-string">&quot;greater&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>p.value<span class="hljs-punctuation">)</span>;<br>        CountTbl<span class="hljs-punctuation">[</span>fmod<span class="hljs-punctuation">,</span> cmod<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>femaleColors <span class="hljs-operator">==</span> femModules<span class="hljs-punctuation">[</span>fmod<span class="hljs-punctuation">]</span> <span class="hljs-operator">&amp;</span> moduleColors <span class="hljs-operator">==</span> consModules<span class="hljs-punctuation">[</span>cmod<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Truncate p values smaller than 10^&#123;-50&#125; to 10^&#123;-50&#125;</span><br>pTable<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.infinite</span><span class="hljs-punctuation">(</span>pTable<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">1.3</span><span class="hljs-operator">*</span><span class="hljs-built_in">max</span><span class="hljs-punctuation">(</span>pTable<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.finite</span><span class="hljs-punctuation">(</span>pTable<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>pTable<span class="hljs-punctuation">[</span>pTable<span class="hljs-operator">&gt;</span><span class="hljs-number">50</span> <span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">50</span> ;<br><span class="hljs-comment"># Marginal counts (really module sizes)</span><br>femModTotals <span class="hljs-operator">=</span> apply<span class="hljs-punctuation">(</span>CountTbl<span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">)</span><br>consModTotals <span class="hljs-operator">=</span> apply<span class="hljs-punctuation">(</span>CountTbl<span class="hljs-punctuation">,</span> <span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#pdf(file = &quot;Plots/ConsensusVsFemaleModules.pdf&quot;, wi = 10, he = 7);</span><br>par<span class="hljs-punctuation">(</span>mfrow<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>par<span class="hljs-punctuation">(</span>cex <span class="hljs-operator">=</span> <span class="hljs-number">1.0</span><span class="hljs-punctuation">)</span>;<br>par<span class="hljs-punctuation">(</span>mar<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> <span class="hljs-number">10.4</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2.7</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><span class="hljs-number">0.3</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Use function labeledHeatmap to produce the color-coded table with all the trimmings</span><br>labeledHeatmap<span class="hljs-punctuation">(</span>Matrix <span class="hljs-operator">=</span> pTable<span class="hljs-punctuation">,</span><br>xLabels <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot; &quot;</span><span class="hljs-punctuation">,</span> consModules<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>yLabels <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot; &quot;</span><span class="hljs-punctuation">,</span> femModules<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>colorLabels <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span><br>xSymbols <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Cons &quot;</span><span class="hljs-punctuation">,</span> consModules<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;: &quot;</span><span class="hljs-punctuation">,</span> consModTotals<span class="hljs-punctuation">,</span> sep<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>ySymbols <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Fem &quot;</span><span class="hljs-punctuation">,</span> femModules<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;: &quot;</span><span class="hljs-punctuation">,</span> femModTotals<span class="hljs-punctuation">,</span> sep<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>textMatrix <span class="hljs-operator">=</span> CountTbl<span class="hljs-punctuation">,</span><br>colors <span class="hljs-operator">=</span> blueWhiteRed<span class="hljs-punctuation">(</span><span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">50</span><span class="hljs-operator">:</span><span class="hljs-number">100</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>main <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Correspondence of Female set-specific and Female-Male consensus modules&quot;</span><span class="hljs-punctuation">,</span><br>cex.text <span class="hljs-operator">=</span> <span class="hljs-number">1.0</span><span class="hljs-punctuation">,</span> cex.lab <span class="hljs-operator">=</span> <span class="hljs-number">1.0</span><span class="hljs-punctuation">,</span> setStdMargins <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span>;<br></code></pre></td></tr></table></figure>

<h2 id="共识模块、基因、性状三者互相关联"><a href="#共识模块、基因、性状三者互相关联" class="headerlink" title="共识模块、基因、性状三者互相关联"></a>共识模块、基因、性状三者互相关联</h2><h3 id="关联网络模块与性状"><a href="#关联网络模块与性状" class="headerlink" title="关联网络模块与性状"></a>关联网络模块与性状</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Set up variables to contain the module-trait correlations</span><br>moduleTraitCor <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br>moduleTraitPvalue <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Calculate the correlations</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> cor<span class="hljs-punctuation">(</span>consMEs<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> use <span class="hljs-operator">=</span> <span class="hljs-string">&quot;p&quot;</span><span class="hljs-punctuation">)</span>;<br>    moduleTraitPvalue<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> corPvalueFisher<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> exprSize<span class="hljs-operator">$</span>nSamples<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-punctuation">&#125;</span><br><span class="hljs-comment"># Convert numerical lables to colors for labeling of modules in the plot</span><br>MEColors <span class="hljs-operator">=</span> labels2colors<span class="hljs-punctuation">(</span><span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>substring<span class="hljs-punctuation">(</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>consMEs<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>MEColorNames <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;ME&quot;</span><span class="hljs-punctuation">,</span> MEColors<span class="hljs-punctuation">,</span> sep<span class="hljs-operator">=</span><span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span>;<br></code></pre></td></tr></table></figure>

<h3 id="可视化"><a href="#可视化" class="headerlink" title="可视化"></a>可视化</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br></pre></td><td class="code"><pre><code class="hljs R">set <span class="hljs-operator">=</span> <span class="hljs-number">1</span><br>textMatrix <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">signif</span><span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;\n(&quot;</span><span class="hljs-punctuation">,</span><br><span class="hljs-built_in">signif</span><span class="hljs-punctuation">(</span>moduleTraitPvalue<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;)&quot;</span><span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>textMatrix<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>par<span class="hljs-punctuation">(</span>mar <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span> <span class="hljs-number">8.8</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2.2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>labeledHeatmap<span class="hljs-punctuation">(</span>Matrix <span class="hljs-operator">=</span> moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>    xLabels <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    yLabels <span class="hljs-operator">=</span> MEColorNames<span class="hljs-punctuation">,</span><br>    ySymbols <span class="hljs-operator">=</span> MEColorNames<span class="hljs-punctuation">,</span><br>    colorLabels <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>    colors <span class="hljs-operator">=</span> blueWhiteRed<span class="hljs-punctuation">(</span><span class="hljs-number">50</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    textMatrix <span class="hljs-operator">=</span> textMatrix<span class="hljs-punctuation">,</span><br>    setStdMargins <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>    cex.text <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span><br>    zlim <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    main <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Module--trait relationships in&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br></pre></td><td class="code"><pre><code class="hljs R">set <span class="hljs-operator">=</span> <span class="hljs-number">2</span><br>textMatrix <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">signif</span><span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;\n(&quot;</span><span class="hljs-punctuation">,</span><br><span class="hljs-built_in">signif</span><span class="hljs-punctuation">(</span>moduleTraitPvalue<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;)&quot;</span><span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>textMatrix<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>par<span class="hljs-punctuation">(</span>mar <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span> <span class="hljs-number">8.8</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2.2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>labeledHeatmap<span class="hljs-punctuation">(</span>Matrix <span class="hljs-operator">=</span> moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>    xLabels <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    yLabels <span class="hljs-operator">=</span> MEColorNames<span class="hljs-punctuation">,</span><br>    ySymbols <span class="hljs-operator">=</span> MEColorNames<span class="hljs-punctuation">,</span><br>    colorLabels <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>    colors <span class="hljs-operator">=</span> blueWhiteRed<span class="hljs-punctuation">(</span><span class="hljs-number">50</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    textMatrix <span class="hljs-operator">=</span> textMatrix<span class="hljs-punctuation">,</span><br>    setStdMargins <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>    cex.text <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span><br>    zlim <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    main <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Module--trait relationships in&quot;</span><span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Initialize matrices to hold the consensus correlation and p-value</span><br>consensusCor <span class="hljs-operator">=</span> matrix<span class="hljs-punctuation">(</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>consensusPvalue <span class="hljs-operator">=</span> matrix<span class="hljs-punctuation">(</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Find consensus negative correlations</span><br>negative <span class="hljs-operator">=</span> moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;</span> <span class="hljs-number">0</span> <span class="hljs-operator">&amp;</span> moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;</span> <span class="hljs-number">0</span>;<br>consensusCor<span class="hljs-punctuation">[</span>negative<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> pmax<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>negative<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>negative<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>consensusPvalue<span class="hljs-punctuation">[</span>negative<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> pmax<span class="hljs-punctuation">(</span>moduleTraitPvalue<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>negative<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> moduleTraitPvalue<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>negative<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># Find consensus positive correlations</span><br>positive <span class="hljs-operator">=</span> moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&gt;</span> <span class="hljs-number">0</span> <span class="hljs-operator">&amp;</span> moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&gt;</span> <span class="hljs-number">0</span>;<br>consensusCor<span class="hljs-punctuation">[</span>positive<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> pmin<span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>positive<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> moduleTraitCor<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>positive<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br>consensusPvalue<span class="hljs-punctuation">[</span>positive<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> pmax<span class="hljs-punctuation">(</span>moduleTraitPvalue<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>positive<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> moduleTraitPvalue<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>positive<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span>;<br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br></pre></td><td class="code"><pre><code class="hljs R">textMatrix <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">signif</span><span class="hljs-punctuation">(</span>consensusCor<span class="hljs-punctuation">,</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;\n(&quot;</span><span class="hljs-punctuation">,</span><br><span class="hljs-built_in">signif</span><span class="hljs-punctuation">(</span>consensusPvalue<span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;)&quot;</span><span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>textMatrix<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>moduleTraitCor<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#pdf(file = &quot;Plots/ModuleTraitRelationships-consensus.pdf&quot;, wi = 10, he = 7);</span><br>par<span class="hljs-punctuation">(</span>mar <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span> <span class="hljs-number">8.8</span><span class="hljs-punctuation">,</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2.2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>labeledHeatmap<span class="hljs-punctuation">(</span>Matrix <span class="hljs-operator">=</span> consensusCor<span class="hljs-punctuation">,</span><br>    xLabels <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    yLabels <span class="hljs-operator">=</span> MEColorNames<span class="hljs-punctuation">,</span><br>    ySymbols <span class="hljs-operator">=</span> MEColorNames<span class="hljs-punctuation">,</span><br>    colorLabels <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>    colors <span class="hljs-operator">=</span> blueWhiteRed<span class="hljs-punctuation">(</span><span class="hljs-number">50</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    textMatrix <span class="hljs-operator">=</span> textMatrix<span class="hljs-punctuation">,</span><br>    setStdMargins <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span><br>    cex.text <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span><br>    zlim <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    main <span class="hljs-operator">=</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Consensus module--trait relationships across\n&quot;</span><span class="hljs-punctuation">,</span><br>    paste<span class="hljs-punctuation">(</span>setLabels<span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&quot; and &quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="导出结果"><a href="#导出结果" class="headerlink" title="导出结果"></a>导出结果</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br></pre></td><td class="code"><pre><code class="hljs R">probes <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><br>consMEs.unord <span class="hljs-operator">=</span> multiSetMEs<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">,</span> universalColors <span class="hljs-operator">=</span> moduleLabels<span class="hljs-punctuation">,</span> excludeGrey <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>GS <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br>kME <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#123;</span><br>GS<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> corAndPvalue<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span>;<br>kME<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> corAndPvalue<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> consMEs.unord<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span>;<br><span class="hljs-punctuation">&#125;</span><br>GS.metaZ <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>GS<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>Z <span class="hljs-operator">+</span> GS<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>Z<span class="hljs-punctuation">)</span><span class="hljs-operator">/</span><span class="hljs-built_in">sqrt</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span>;<br>kME.metaZ <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>kME<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>Z <span class="hljs-operator">+</span> kME<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>Z<span class="hljs-punctuation">)</span><span class="hljs-operator">/</span><span class="hljs-built_in">sqrt</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span>;<br>GS.metaP <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-operator">*</span>pnorm<span class="hljs-punctuation">(</span><span class="hljs-built_in">abs</span><span class="hljs-punctuation">(</span>GS.metaZ<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> lower.tail <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span>;<br>kME.metaP <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-operator">*</span>pnorm<span class="hljs-punctuation">(</span><span class="hljs-built_in">abs</span><span class="hljs-punctuation">(</span>kME.metaZ<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> lower.tail <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span>;<br>GSmat <span class="hljs-operator">=</span> rbind<span class="hljs-punctuation">(</span>GS<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>cor<span class="hljs-punctuation">,</span> GS<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>cor<span class="hljs-punctuation">,</span> GS<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>p<span class="hljs-punctuation">,</span> GS<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>p<span class="hljs-punctuation">,</span> GS.metaZ<span class="hljs-punctuation">,</span> GS.metaP<span class="hljs-punctuation">)</span>;<br>nTraits <span class="hljs-operator">=</span> checkSets<span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>nGenes<br>traitNames <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>GSmat<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>nGenes<span class="hljs-punctuation">,</span> <span class="hljs-number">6</span><span class="hljs-operator">*</span>nTraits<span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>GSmat<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> probes;<br>colnames<span class="hljs-punctuation">(</span>GSmat<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> spaste<span class="hljs-punctuation">(</span><br><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;GS.set1.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;GS.set2.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;p.GS.set1.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;p.GS.set2.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Z.GS.meta.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;p.GS.meta&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>traitNames<span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span> nTraits<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># Same code for kME:</span><br>kMEmat <span class="hljs-operator">=</span> rbind<span class="hljs-punctuation">(</span>kME<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>cor<span class="hljs-punctuation">,</span> kME<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>cor<span class="hljs-punctuation">,</span> kME<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>p<span class="hljs-punctuation">,</span> kME<span class="hljs-punctuation">[[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>p<span class="hljs-punctuation">,</span> kME.metaZ<span class="hljs-punctuation">,</span> kME.metaP<span class="hljs-punctuation">)</span>;<br>MEnames <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>consMEs.unord<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span>;<br>nMEs <span class="hljs-operator">=</span> checkSets<span class="hljs-punctuation">(</span>consMEs.unord<span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>nGenes<br><span class="hljs-built_in">dim</span><span class="hljs-punctuation">(</span>kMEmat<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>nGenes<span class="hljs-punctuation">,</span> <span class="hljs-number">6</span><span class="hljs-operator">*</span>nMEs<span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>kMEmat<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> probes;<br>colnames<span class="hljs-punctuation">(</span>kMEmat<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> spaste<span class="hljs-punctuation">(</span><br><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;kME.set1.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;kME.set2.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;p.kME.set1.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;p.kME.set2.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Z.kME.meta.&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;p.kME.meta&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>MEnames<span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span> nMEs<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs R">info <span class="hljs-operator">=</span> data.frame<span class="hljs-punctuation">(</span>Probe <span class="hljs-operator">=</span> probes<span class="hljs-punctuation">,</span><br>            ModuleLabel <span class="hljs-operator">=</span> moduleLabels<span class="hljs-punctuation">,</span><br>            ModuleColor <span class="hljs-operator">=</span> labels2colors<span class="hljs-punctuation">(</span>moduleLabels<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>            GSmat<span class="hljs-punctuation">,</span><br>            kMEmat<span class="hljs-punctuation">)</span>;<br>info<br></code></pre></td></tr></table></figure>

<h2 id="比较两者的WGCNA网络"><a href="#比较两者的WGCNA网络" class="headerlink" title="比较两者的WGCNA网络"></a>比较两者的WGCNA网络</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment"># Create a variable weight that will hold just the body weight of mice in both sets</span><br>weight <span class="hljs-operator">=</span> vector<span class="hljs-punctuation">(</span>mode <span class="hljs-operator">=</span> <span class="hljs-string">&quot;list&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span> <span class="hljs-operator">=</span> nSets<span class="hljs-punctuation">)</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>set <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nSets<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    weight<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> as.data.frame<span class="hljs-punctuation">(</span>Traits<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-operator">$</span>weight_g<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>    <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>weight<span class="hljs-punctuation">[[</span>set<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">=</span> <span class="hljs-string">&quot;weight&quot;</span><br><span class="hljs-punctuation">&#125;</span><br><span class="hljs-comment"># Recalculate consMEs to give them color names</span><br>consMEsC <span class="hljs-operator">=</span> multiSetMEs<span class="hljs-punctuation">(</span>multiExpr<span class="hljs-punctuation">,</span> universalColors <span class="hljs-operator">=</span> moduleColors<span class="hljs-punctuation">)</span>;<br><span class="hljs-comment"># We add the weight trait to the eigengenes and order them by consesus hierarchical clustering:</span><br>MET <span class="hljs-operator">=</span> consensusOrderMEs<span class="hljs-punctuation">(</span>addTraitToMEs<span class="hljs-punctuation">(</span>consMEsC<span class="hljs-punctuation">,</span> weight<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>plotEigengeneNetworks<span class="hljs-punctuation">(</span>MET<span class="hljs-punctuation">,</span> setLabels<span class="hljs-punctuation">,</span> marDendro <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> marHeatmap <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    zlimPreservation <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> xLabelsAngle <span class="hljs-operator">=</span> <span class="hljs-number">90</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

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