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            <h1 id="seo-header">Cmap药物数据库使用记录</h1>
            
            
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                <p>Connectivity Map（Cmap）为一个基因表达数据库，由哈佛、剑桥大学和麻省理工学院研究人员构建，利用不同干扰物（包括小分子）处理人类细胞后的基因表达差异，建立一个干扰物、基因表达和疾病相互关联的生物应用数据库。研究团队认为以基因表达谱所建立的基因、疾病与药物的关联性，可协助研究者在药物研发领域上，快速利用基因表达谱数据比对出与疾病高相关性的药物、推论大部分药物分子的主要结构，并能够归纳出药物分子可能的作用机制。（知乎 <a target="_blank" rel="noopener" href="https://www.zhihu.com/people/gpf-64">FrontScience科研</a>）</p>
<h2 id="导出差异基因"><a href="#导出差异基因" class="headerlink" title="导出差异基因"></a>导出差异基因</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></pre></td><td class="code"><pre><code class="hljs R">x <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>up <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> log2FoldChange <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>up <span class="hljs-operator">&lt;-</span> head<span class="hljs-punctuation">(</span>up<span class="hljs-punctuation">,</span> <span class="hljs-number">150</span><span class="hljs-punctuation">)</span><br>down <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> log2FoldChange <span class="hljs-operator">&lt;</span> <span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>down <span class="hljs-operator">&lt;-</span> tail<span class="hljs-punctuation">(</span>down<span class="hljs-punctuation">,</span> <span class="hljs-number">150</span><span class="hljs-punctuation">)</span><br>up <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>up<span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">)</span><br>down <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>down<span class="hljs-operator">$</span>gene_name<span class="hljs-punctuation">)</span><br>write.table<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> as.data.frame<span class="hljs-punctuation">(</span>up<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;cmap_input_up.txt&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">quote</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>write.table<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> as.data.frame<span class="hljs-punctuation">(</span>down<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;cmap_input_down.txt&#x27;</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">quote</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="进行Cmap分析"><a href="#进行Cmap分析" class="headerlink" title="进行Cmap分析"></a>进行Cmap分析</h2><p><img src="https://img-cdn.limour.top/2022/09/03/63133cc60e6e1.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></p>
<p><a target="_blank" rel="noopener" href="https://clue.io/query">点此进入分析页面</a>，完成后可下载tar.gz的结果，解压后arfs&#x2F;TAG下面的gct是我们需要的</p>
<h2 id="对结果进行可视化"><a href="#对结果进行可视化" class="headerlink" title="对结果进行可视化"></a>对结果进行可视化</h2><h3 id="读取数据"><a href="#读取数据" class="headerlink" title="读取数据"></a>读取数据</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></pre></td><td class="code"><pre><code class="hljs R">cmap <span class="hljs-operator">&lt;-</span> read.table<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;query_result.gct&#x27;</span><span class="hljs-punctuation">,</span> header <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> sep <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\t&#x27;</span><span class="hljs-punctuation">,</span> allowEscapes <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">quote</span> <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">,</span> comment.char <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;#&#x27;</span><span class="hljs-punctuation">,</span> skip<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br>cmap <span class="hljs-operator">&lt;-</span> cmap<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>saveRDS<span class="hljs-punctuation">(</span>cmap<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cmap_query_result.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<ul>
<li>pert_iname  干扰物命名(化合物或者基因名)</li>
<li>cell_iname 细胞系名</li>
<li>pert_type 干扰类型(化合物&#x2F;基因敲除、过表达)</li>
<li>pert_idose 剂量</li>
<li>pert_itime 时间</li>
<li>nsample 样本数</li>
<li>cc_q75 重复相同实验的结果相似度指标</li>
<li>ss_ngene 干扰影响强度指标</li>
<li>tas 综合cc_q75与ss的评价指标结果</li>
<li>raw_cs 连通性分数</li>
</ul>
<h3 id="清洗数据"><a href="#清洗数据" class="headerlink" title="清洗数据"></a>清洗数据</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">test <span class="hljs-operator">&lt;-</span> cmap<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pert_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cell_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;tas&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;raw_cs&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;fdr_q_nlog10&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>test<span class="hljs-operator">$</span>tas <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>test<span class="hljs-operator">$</span>tas<span class="hljs-punctuation">)</span><br>test<span class="hljs-operator">$</span>raw_cs <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>test<span class="hljs-operator">$</span>raw_cs<span class="hljs-punctuation">)</span><br>test<span class="hljs-operator">$</span>fdr_q_nlog10 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>test<span class="hljs-operator">$</span>fdr_q_nlog10<span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> tail<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> <span class="hljs-number">100</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="绘图"><a href="#绘图" class="headerlink" title="绘图"></a>绘图</h3><h4 id="点图"><a href="#点图" class="headerlink" title="点图"></a>点图</h4><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">library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">20</span><span class="hljs-punctuation">)</span><br>p <span class="hljs-operator">&lt;-</span> ggplot<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> aes<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> cell_iname<span class="hljs-punctuation">,</span> y <span class="hljs-operator">=</span> pert_iname<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> geom_point<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span>fdr_q_nlog10<span class="hljs-punctuation">,</span>color<span class="hljs-operator">=</span>raw_cs<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> scale_size<span class="hljs-punctuation">(</span><span class="hljs-built_in">range</span> <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span><span class="hljs-number">10</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> scale_colour_gradient2<span class="hljs-punctuation">(</span>low<span class="hljs-operator">=</span>rgb<span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span> <span class="hljs-punctuation">,</span>high<span class="hljs-operator">=</span>rgb<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> mid <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;white&#x27;</span><span class="hljs-punctuation">)</span><br>p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme_bw<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.text<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                            axis.title<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <br>                            axis.text.x<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>angle<span class="hljs-operator">=</span><span class="hljs-number">90</span><span class="hljs-punctuation">,</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span>vjust<span class="hljs-operator">=</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>p<br></code></pre></td></tr></table></figure>

<h4 id="热图"><a href="#热图" class="headerlink" title="热图"></a>热图</h4><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">f_long2wide <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> colN<span class="hljs-punctuation">,</span> rowN<span class="hljs-punctuation">,</span> valueN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    rowR <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>rowN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    colR <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>colN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> matrix<span class="hljs-punctuation">(</span>nrow<span class="hljs-operator">=</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>rowR<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol<span class="hljs-operator">=</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>colR<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>    resN <span class="hljs-operator">&lt;-</span> matrix<span class="hljs-punctuation">(</span>nrow<span class="hljs-operator">=</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>rowR<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol<span class="hljs-operator">=</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>colR<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>    rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> rowR<br>    colnames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> colR<br>    rownames<span class="hljs-punctuation">(</span>resN<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> rowR<br>    colnames<span class="hljs-punctuation">(</span>resN<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> colR<br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nrow<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-punctuation">[</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>rowN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>colN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> res<span class="hljs-punctuation">[</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>rowN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>colN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">+</span> df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span> valueN<span class="hljs-punctuation">]</span><br>        resN<span class="hljs-punctuation">[</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>rowN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>colN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> resN<span class="hljs-punctuation">[</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>rowN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span>colN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">+</span> <span class="hljs-number">1</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res <span class="hljs-operator">&lt;-</span> res <span class="hljs-operator">/</span> resN<br>    res<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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>ComplexHeatmap<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>circlize<span class="hljs-punctuation">)</span><br>col_fun <span class="hljs-operator">&lt;-</span> colorRamp2<span class="hljs-punctuation">(</span><br>  <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">0</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><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;#BC3C29AA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;white&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;#99CCCCAA&quot;</span><span class="hljs-punctuation">)</span><br>  <span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> cmap<span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pert_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cell_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;tas&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;raw_cs&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;fdr_q_nlog10&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>test<span class="hljs-operator">$</span>fdr_q_nlog10 <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>test<span class="hljs-operator">$</span>fdr_q_nlog10<span class="hljs-punctuation">)</span><br>test<span class="hljs-operator">$</span>raw_cs <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>test<span class="hljs-operator">$</span>raw_cs<span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> cell_iname <span class="hljs-operator">%in%</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;LNCAP&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;PC3&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;VCAP&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>mat <span class="hljs-operator">&lt;-</span> f_long2wide<span class="hljs-punctuation">(</span>tail<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cell_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;pert_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;raw_cs&#x27;</span><span class="hljs-punctuation">)</span><br>mat_tmp <span class="hljs-operator">&lt;-</span> f_long2wide<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cell_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;pert_iname&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;raw_cs&#x27;</span><span class="hljs-punctuation">)</span><br>mat <span class="hljs-operator">&lt;-</span> mat_tmp<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>mat<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.nan</span><span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> <span class="hljs-number">0</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">4</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><br>Heatmap<span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">,</span> col<span class="hljs-operator">=</span>col_fun<span class="hljs-punctuation">,</span> name <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;raw_cs&#x27;</span><span class="hljs-punctuation">,</span> row_order<span class="hljs-operator">=</span>nrow<span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">)</span><span class="hljs-operator">:</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> column_order <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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