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            <h1 id="seo-header">绘制富集系统聚类图（简化版）</h1>
            
            
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                <p>之前用<a href="https://occdn.limour.top/2315.html">GOplot绘制了富集系统聚类图</a>，感觉非常好看也非常实用，因此简化一下调用流程</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><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">f_GOplot <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>GOplotIn<span class="hljs-punctuation">,</span> genedata<span class="hljs-punctuation">,</span> filePath<span class="hljs-punctuation">,</span> Category<span class="hljs-operator">=</span><span class="hljs-string">&#x27;enricher&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>GOplotIn<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Term&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;adj_pval&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Genes&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-comment">#修改列名,后面弦图绘制的时候需要这样的格式</span><br>    GOplotIn<span class="hljs-operator">$</span>Genes <span class="hljs-operator">&lt;-</span> stringr<span class="hljs-operator">::</span>str_replace_all<span class="hljs-punctuation">(</span>GOplotIn<span class="hljs-operator">$</span>Genes<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;/&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;,&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#把GeneID列中的’/’替换成‘,’</span><br>    GOplotIn<span class="hljs-operator">$</span>Category <span class="hljs-operator">=</span> Category <span class="hljs-comment">#分类信息</span><br>    circ <span class="hljs-operator">&lt;-</span> GOplot<span class="hljs-operator">::</span>circle_dat<span class="hljs-punctuation">(</span>GOplotIn<span class="hljs-punctuation">,</span> genedata<span class="hljs-punctuation">)</span> <span class="hljs-comment">#GOplot导入数据格式整理</span><br>    chord <span class="hljs-operator">&lt;&lt;-</span> GOplot<span class="hljs-operator">::</span>chord_dat<span class="hljs-punctuation">(</span>data <span class="hljs-operator">=</span> circ<span class="hljs-punctuation">,</span>genes <span class="hljs-operator">=</span> genedata<span class="hljs-punctuation">)</span> <span class="hljs-comment">#生成含有选定基因的数据框</span><br>    pdf<span class="hljs-punctuation">(</span>filePath<span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> width<span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> height<span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>GOplot<span class="hljs-operator">::</span>GOCluster<span class="hljs-punctuation">(</span>circ<span class="hljs-punctuation">,</span> GOplotIn<span class="hljs-operator">$</span>Term<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#系统聚类图</span><br>    dev.off<span class="hljs-punctuation">(</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></pre></td><td class="code"><pre><code class="hljs R">write.csv<span class="hljs-punctuation">(</span>res_MF<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-string">&#x27;ID&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Description&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;p.adjust&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;geneID&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;res_MF.csv&#x27;</span><span class="hljs-punctuation">)</span><br> <br>DEG <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;DEG_filer.rds&#x27;</span><span class="hljs-punctuation">)</span><br>genedata<span class="hljs-operator">&lt;-</span>data.frame<span class="hljs-punctuation">(</span>ID<span class="hljs-operator">=</span>DEG<span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">,</span>logFC<span class="hljs-operator">=</span>DEG<span class="hljs-operator">$</span>log2FoldChange<span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;res_MF.csv&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>f_GOplot<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> genedata<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;test.pdf&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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