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  245.             <h1 id="seo-header">Seurat (七) 判断某个细胞群的性质 (一) ——GSEA分析</h1>
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  250.                 <h2 id="第一步-读取数据"><a href="#第一步-读取数据" class="headerlink" title="第一步 读取数据"></a>第一步 读取数据</h2><figure class="highlight gauss"><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></pre></td><td class="code"><pre><code class="hljs gauss"><span class="hljs-keyword">library</span>(Matrix)<br><span class="hljs-keyword">library</span>(Seurat)<br><span class="hljs-keyword">library</span>(plyr)<br><span class="hljs-keyword">library</span>(dplyr)<br><span class="hljs-keyword">library</span>(patchwork)<br><span class="hljs-keyword">library</span>(purrr)<br> <br><span class="hljs-built_in">rm</span>(list = <span class="hljs-built_in">ls</span>())<br><span class="hljs-meta"># 配置数据路径</span><br>root_path = <span class="hljs-string">&quot;~/zlliu/R_data/TCGA&quot;</span><br> <br><span class="hljs-meta"># 配置结果保存路径</span><br>output_path = root_path<br><span class="hljs-keyword">if</span> (!file.exists(output_path))&#123;dir.create(output_path)&#125;<br> <br><span class="hljs-meta"># 设置工作目录，输出文件将保存在此目录下</span><br><span class="hljs-built_in">setwd</span>(output_path)<br><span class="hljs-built_in">getwd</span>()<br><br></code></pre></td></tr></table></figure>
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  251. 

  252. <h2 id="第一步-得到指定群的差异基因"><a href="#第一步-得到指定群的差异基因" class="headerlink" title="第一步 得到指定群的差异基因"></a>第一步 得到指定群的差异基因</h2><figure class="highlight stylus"><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 stylus">scRNA<span class="hljs-selector-attr">[[<span class="hljs-string">&#x27;manual_3&#x27;</span>]</span>] = <span class="hljs-built_in">ifelse</span>(scRNA<span class="hljs-selector-attr">[[<span class="hljs-string">&#x27;manual_2&#x27;</span>]</span>] == <span class="hljs-string">&quot;Unkown_10&quot;</span>, <span class="hljs-string">&quot;Unkown_10&quot;</span>, <span class="hljs-string">&#x27;others&#x27;</span>)<br><span class="hljs-function"><span class="hljs-title">Idents</span><span class="hljs-params">(scRNA)</span></span> &lt;- scRNA<span class="hljs-selector-attr">[[<span class="hljs-string">&#x27;manual_3&#x27;</span>]</span>]<br>all_markers &lt;- <span class="hljs-built_in">FindAllMarkers</span>(scRNA, min<span class="hljs-selector-class">.pct</span> = <span class="hljs-number">0.25</span>, logfc<span class="hljs-selector-class">.threshold</span> = <span class="hljs-number">0.25</span>)<br>significant_markers &lt;- <span class="hljs-built_in">subset</span>(all_markers, subset = p_val_adj&lt;<span class="hljs-number">0.05</span>)<br>write<span class="hljs-selector-class">.csv</span>(significant_markers, <span class="hljs-string">&#x27;manual_2_Markers.csv&#x27;</span>)<br>significant_markers &lt;- <span class="hljs-built_in">subset</span>(significant_markers, cluster==<span class="hljs-string">&quot;Unkown_10&quot;</span>)<br><span class="hljs-function"><span class="hljs-title">rownames</span><span class="hljs-params">(significant_markers)</span></span> &lt;- <span class="hljs-built_in">gsub</span>(<span class="hljs-string">&quot;\\.(\\.?\\d*)&quot;</span>,<span class="hljs-string">&quot;&quot;</span>,<span class="hljs-built_in">rownames</span>(significant_markers))<br>fc &lt;- <span class="hljs-built_in">with</span>(significant_markers, <span class="hljs-built_in">mean</span>(<span class="hljs-built_in">abs</span>(avg_log2FC)) + <span class="hljs-number">1</span>*<span class="hljs-built_in">sd</span>(<span class="hljs-built_in">abs</span>(avg_log2FC)))<br>usignificant_markers &lt;- <span class="hljs-built_in">subset</span>(significant_markers, avg_log2FC&gt;fc)<br>dsignificant_markers &lt;- <span class="hljs-built_in">subset</span>(significant_markers, avg_log2FC&lt;fc)<br></code></pre></td></tr></table></figure>
    253. 

  253. 

  254. <h2 id="第二步-KEGG"><a href="#第二步-KEGG" class="headerlink" title="第二步 KEGG"></a>第二步 KEGG</h2><figure class="highlight lua"><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><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br></pre></td><td class="code"><pre><code class="hljs lua"># clusterProfiler作kegg富集分析<br>library(clusterProfiler)<br>library(enrichplot)<br>library(forcats)<br><br>f_id2name_fuck &lt;- <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(lc_exp, lc_db)</span></span>&#123;<br>    <span class="hljs-keyword">if</span>(!is.data.frame(lc_db))&#123;<br>        lc_ids &lt;- toTable(lc_db)<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        lc_ids &lt;- lc_db<br>    &#125;<br>    res_n &lt;- rownames(lc_exp)<br>    res_n &lt;- res_n[res_n %<span class="hljs-keyword">in</span>% lc_ids<span class="hljs-string">[[1]]</span>]<br>    res &lt;- lc_exp[res_n,]<br>    <span class="hljs-keyword">if</span>(!is.data.frame(res))&#123;res=data.frame(row.names = res_n, res)&#125;<br>    lc_ids=lc_ids[<span class="hljs-built_in">match</span>(rownames(res),lc_ids<span class="hljs-string">[[1]]</span>),]<br>    lc_tmp = by(res,<br>         lc_ids<span class="hljs-string">[[2]]</span>,<br>         <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(x)</span></span> rownames(x)[which.<span class="hljs-built_in">max</span>(rowMeans(x))])<br>    lc_probes = as.character(lc_tmp)<br>    res_n &lt;- rownames(res)<br>    res_n &lt;- res_n[res_n %<span class="hljs-keyword">in</span>% lc_probes]<br>    res = res[res_n,]<br>    <span class="hljs-keyword">if</span>(!is.data.frame(res))&#123;res=data.frame(row.names = res_n, res)&#125;  <br>    rownames(res)=lc_ids[<span class="hljs-built_in">match</span>(rownames(res),lc_ids<span class="hljs-string">[[1]]</span>),<span class="hljs-number">2</span>]<br>    res<br>&#125;<br><br>library(org.Hs.eg.db)<br>f_id2name_sb &lt;- <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(lc_cgene, keytype=&quot;SYMBOL&quot;, columns=&quot;ENTREZID&quot;)</span></span>&#123;<br>    res=<span class="hljs-built_in">select</span>(org.Hs.eg.db,keys=lc_cgene,columns=columns, keytype=keytype)<br>    res &lt;- subset(res, !is.na(ENTREZID))<br>    res$ENTREZID<br>&#125;<br><br>library(ggplot2)<br>library(DOSE)<br>f_kegg_p &lt;- <span class="hljs-function"><span class="hljs-keyword">function</span><span class="hljs-params">(keggr2, n = 15)</span></span>&#123;<br>    keggr &lt;- subset(keggr2@result, p.adjust &lt; <span class="hljs-number">0.05</span>)<br>    keggr<span class="hljs-string">[[&#x27;-log(Padj)&#x27;]]</span> &lt;- -<span class="hljs-built_in">log10</span>(keggr<span class="hljs-string">[[&#x27;p.adjust&#x27;]]</span>)<br>    keggr<span class="hljs-string">[[&#x27;geneRatio&#x27;]]</span> &lt;- parse_ratio(keggr<span class="hljs-string">[[&#x27;GeneRatio&#x27;]]</span>)<br>    keggr$Description &lt;- factor(keggr$Description, <br>                                       levels=keggr[order(keggr$geneRatio),]$Description)<br>    ggplot(head(keggr,n),aes(x=geneRatio,y=Description))+<br>        geom_point(aes(color=`-<span class="hljs-built_in">log</span>(Padj)`,<br>                 size=`Count`))+<br>        theme_bw()+<br>        scale_color_gradient(low=<span class="hljs-string">&quot;blue1&quot;</span>,high=<span class="hljs-string">&quot;brown1&quot;</span>)+<br>        labs(y=NULL) + <br>        theme(axis.text.x=element_text(angle=<span class="hljs-number">90</span>,hjust = <span class="hljs-number">1</span>,vjust=<span class="hljs-number">0.5</span>, size = <span class="hljs-number">12</span>),<br>             axis.text.y=element_text(size = <span class="hljs-number">15</span>))<br>&#125;<br><br></code></pre></td></tr></table></figure>
    255. 

  255. 

  256. <figure class="highlight isbl"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs isbl"><span class="hljs-variable">ENTREZID</span>=<span class="hljs-function"><span class="hljs-title">f_id2name_sb</span>(<span class="hljs-title">rownames</span>(<span class="hljs-variable">scRNA</span>))</span><br></code></pre></td></tr></table></figure>
    257. 

  257. 

  258. <figure class="highlight stylus"><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 stylus">kegg<span class="hljs-selector-class">.u</span> &lt;- <span class="hljs-built_in">enrichKEGG</span>(gene = <span class="hljs-built_in">f_id2name_sb</span>(usignificant_markers<span class="hljs-variable">$gene</span>),<br>      organism = <span class="hljs-built_in">search_kegg_organism</span>(<span class="hljs-string">&#x27;Homo sapiens&#x27;</span>)<span class="hljs-variable">$kegg_code</span>,<br>      universe = ENTREZID,<br>      pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>,<br>      qvalueCutoff =<span class="hljs-number">0.05</span>)<br><br></code></pre></td></tr></table></figure>
    259. 

  259. 

  260. <figure class="highlight reasonml"><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 reasonml">f<span class="hljs-constructor">_kegg_p(<span class="hljs-params">kegg</span>.<span class="hljs-params">u</span>, <span class="hljs-params">n</span> =15)</span> %&gt;% f<span class="hljs-constructor">_title(<span class="hljs-string">&quot;kegg.u&quot;</span>)</span><br>f<span class="hljs-constructor">_kegg_p(<span class="hljs-params">kegg</span>.<span class="hljs-params">d</span>, <span class="hljs-params">n</span> =15)</span> %&gt;% f<span class="hljs-constructor">_title(<span class="hljs-string">&quot;kegg.d&quot;</span>)</span><br></code></pre></td></tr></table></figure>
    261. 

  261. 

  262. <p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/10/kegg.u.png"><img src="https://img-cdn.limour.top/blog_wp/2021/10/kegg.u.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
    263. 

  263. <h2 id="第三步-GO"><a href="#第三步-GO" class="headerlink" title="第三步 GO"></a>第三步 GO</h2><figure class="highlight stylus"><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></pre></td><td class="code"><pre><code class="hljs stylus">GO<span class="hljs-selector-class">.U</span><span class="hljs-selector-class">.CC</span> &lt;- <span class="hljs-built_in">enrichGO</span>(gene = <span class="hljs-built_in">f_id2name_sb</span>(usignificant_markers<span class="hljs-variable">$gene</span>),<br>                    keyType = <span class="hljs-string">&quot;ENTREZID&quot;</span>,<br>                   OrgDb= <span class="hljs-string">&#x27;org.Hs.eg.db&#x27;</span>,<br>                   ont = <span class="hljs-string">&quot;CC&quot;</span>,<br>                   universe = ENTREZID,<br>                   pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>,<br>                   qvalueCutoff = <span class="hljs-number">0.05</span>,<br>                   readable = TRUE)<br>GO<span class="hljs-selector-class">.U</span><span class="hljs-selector-class">.BP</span> &lt;- <span class="hljs-built_in">enrichGO</span>(gene = <span class="hljs-built_in">f_id2name_sb</span>(usignificant_markers<span class="hljs-variable">$gene</span>),<br>                    keyType = <span class="hljs-string">&quot;ENTREZID&quot;</span>,<br>                   OrgDb= <span class="hljs-string">&#x27;org.Hs.eg.db&#x27;</span>,<br>                   ont = <span class="hljs-string">&quot;BP&quot;</span>,<br>                   universe = ENTREZID,<br>                   pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>,<br>                   qvalueCutoff = <span class="hljs-number">0.05</span>,<br>                   readable = TRUE)<br>GO<span class="hljs-selector-class">.U</span><span class="hljs-selector-class">.MF</span> &lt;- <span class="hljs-built_in">enrichGO</span>(gene = <span class="hljs-built_in">f_id2name_sb</span>(usignificant_markers<span class="hljs-variable">$gene</span>),<br>                    keyType = <span class="hljs-string">&quot;ENTREZID&quot;</span>,<br>                   OrgDb= <span class="hljs-string">&#x27;org.Hs.eg.db&#x27;</span>,<br>                   ont = <span class="hljs-string">&quot;MF&quot;</span>,<br>                   universe = ENTREZID,<br>                   pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>,<br>                   qvalueCutoff = <span class="hljs-number">0.05</span>,<br>                   readable = TRUE)<br><br></code></pre></td></tr></table></figure>
    264. 

  264. 

  265. <figure class="highlight gcode"><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></pre></td><td class="code"><pre><code class="hljs gcode">f_kegg_p<span class="hljs-comment">(GO.U.CC, n =15)</span> <span class="hljs-meta">%</span>&gt;<span class="hljs-meta">%</span> f_title<span class="hljs-comment">(&quot;GO.U.CC&quot;)</span><br>f_kegg_p<span class="hljs-comment">(GO.U.BP, n =15)</span> <span class="hljs-meta">%</span>&gt;<span class="hljs-meta">%</span> f_title<span class="hljs-comment">(&quot;GO.U.BP&quot;)</span><br>f_kegg_p<span class="hljs-comment">(GO.U.MF, n =15)</span> <span class="hljs-meta">%</span>&gt;<span class="hljs-meta">%</span> f_title<span class="hljs-comment">(&quot;GO.U.MF&quot;)</span><br><br></code></pre></td></tr></table></figure>
    266. 

  266. 

  267. <h2 id="第四步-GESA"><a href="#第四步-GESA" class="headerlink" title="第四步 GESA"></a>第四步 GESA</h2><figure class="highlight stylus"><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 stylus">f_gse_fuck &lt;- <span class="hljs-built_in">function</span>(geneSym, logFC, keytype=<span class="hljs-string">&quot;SYMBOL&quot;</span>, <span class="hljs-attribute">columns</span>=<span class="hljs-string">&quot;ENTREZID&quot;</span>, lc_order=T)&#123;<br>    res=<span class="hljs-built_in">select</span>(org<span class="hljs-selector-class">.Hs</span><span class="hljs-selector-class">.eg</span><span class="hljs-selector-class">.db</span>,keys=geneSym,<span class="hljs-attribute">columns</span>=columns, keytype=keytype)<br>    res &lt;- <span class="hljs-built_in">cbind</span>(res, logFC)<br>    res &lt;- <span class="hljs-built_in">subset</span>(res, !is<span class="hljs-selector-class">.na</span>(ENTREZID))<br>    <span class="hljs-built_in">if</span>(lc_order)&#123;res &lt;- res<span class="hljs-selector-attr">[order(res$logFC, decreasing = T),]</span>&#125;<br>    res2 &lt;- res<span class="hljs-variable">$logFC</span><br>    <span class="hljs-built_in">if</span>(lc_order)&#123;<br>        <span class="hljs-built_in">names</span>(res2) &lt;- res<span class="hljs-selector-attr">[[columns]</span>]<br>    &#125;<span class="hljs-keyword">else</span>&#123;<br>        <span class="hljs-built_in">names</span>(res2) &lt;- res<span class="hljs-selector-attr">[[keytype]</span>]<br>    &#125;<br>    res2<br>&#125;<br></code></pre></td></tr></table></figure>
    268. 

  268. 

  269. <figure class="highlight nginx"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs nginx"><span class="hljs-attribute">lgene</span> &lt;- f_gse_fuck(significant_markers<span class="hljs-variable">$gene</span>,significant_markers<span class="hljs-variable">$avg_log2FC</span>)<br></code></pre></td></tr></table></figure>
    270. 

  270. 

  271. <figure class="highlight stylus"><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 stylus">gsekegg &lt;- <span class="hljs-built_in">gseKEGG</span>(gene = lgene,<br>      organism = <span class="hljs-built_in">search_kegg_organism</span>(<span class="hljs-string">&#x27;Homo sapiens&#x27;</span>)<span class="hljs-variable">$kegg_code</span>,<br>      pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>)<br><br>GO<span class="hljs-selector-class">.CC</span> &lt;- <span class="hljs-built_in">gseGO</span>(gene = lgene,<br>                   keyType = <span class="hljs-string">&quot;ENTREZID&quot;</span>,<br>                   OrgDb= org<span class="hljs-selector-class">.Hs</span><span class="hljs-selector-class">.eg</span><span class="hljs-selector-class">.db</span>,<br>                   ont = <span class="hljs-string">&quot;CC&quot;</span>,<br>                   pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>)<br><br>GO<span class="hljs-selector-class">.BP</span> &lt;- <span class="hljs-built_in">gseGO</span>(gene = lgene,<br>                   keyType = <span class="hljs-string">&quot;ENTREZID&quot;</span>,<br>                   OrgDb= org<span class="hljs-selector-class">.Hs</span><span class="hljs-selector-class">.eg</span><span class="hljs-selector-class">.db</span>,<br>                   ont = <span class="hljs-string">&quot;CC&quot;</span>,<br>                   pAdjustMethod = <span class="hljs-string">&quot;fdr&quot;</span>)<br><br></code></pre></td></tr></table></figure>
    272. 

  272. 

  273. <figure class="highlight less"><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 less"><span class="hljs-selector-tag">options</span>(repr.plot.width=<span class="hljs-number">9</span>, repr.plot.height=<span class="hljs-number">9</span>)<br><span class="hljs-selector-tag">gseaplot2</span>(gsekegg,geneSetID=<span class="hljs-built_in">head</span>(<span class="hljs-built_in">which</span>(gsekegg<span class="hljs-variable">@result</span>$enrichmentScore&gt;<span class="hljs-number">0.4</span>),<span class="hljs-number">15</span>))<br><span class="hljs-selector-tag">gseaplot2</span>(gsekegg,geneSetID=<span class="hljs-built_in">head</span>(<span class="hljs-built_in">which</span>(gsekegg<span class="hljs-variable">@result</span>$enrichmentScore &lt; -<span class="hljs-number">0.3</span>),<span class="hljs-number">6</span>))<br><br><span class="hljs-selector-tag">gseaplot2</span>(GO.CC,geneSetID=<span class="hljs-built_in">head</span>(<span class="hljs-built_in">which</span>(GO.CC<span class="hljs-variable">@result</span>$enrichmentScore&gt;<span class="hljs-number">0.4</span>),<span class="hljs-number">15</span>))<br><span class="hljs-selector-tag">gseaplot2</span>(GO.CC,geneSetID=<span class="hljs-built_in">head</span>(<span class="hljs-built_in">which</span>(GO.CC<span class="hljs-variable">@result</span>$enrichmentScore &lt; -<span class="hljs-number">0.3</span>),<span class="hljs-number">6</span>))<br><br><span class="hljs-selector-tag">gseaplot2</span>(GO.BP,geneSetID=<span class="hljs-built_in">head</span>(<span class="hljs-built_in">which</span>(GO.BP<span class="hljs-variable">@result</span>$enrichmentScore&gt;<span class="hljs-number">0.4</span>),<span class="hljs-number">15</span>))<br><span class="hljs-selector-tag">gseaplot2</span>(GO.BP,geneSetID=<span class="hljs-built_in">head</span>(<span class="hljs-built_in">which</span>(GO.BP<span class="hljs-variable">@result</span>$enrichmentScore &lt; -<span class="hljs-number">0.3</span>),<span class="hljs-number">6</span>))<br><br></code></pre></td></tr></table></figure>
    274. 

  274. 

  275. <p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/10/kegg.gse_.png"><img src="https://img-cdn.limour.top/blog_wp/2021/10/kegg.gse_.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
    276. 

  276. <h2 id="第五步-GO-terms关系网络图"><a href="#第五步-GO-terms关系网络图" class="headerlink" title="第五步 GO terms关系网络图"></a>第五步 GO terms关系网络图</h2><figure class="highlight scss"><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 scss"># <span class="hljs-built_in">options</span>(BioC_mirror=&quot;https://mirrors.tuna.tsinghua.edu.cn/bioconductor&quot;)<br># BiocManager::<span class="hljs-built_in">install</span>(<span class="hljs-string">&quot;ggnewscale&quot;</span>)<br><span class="hljs-built_in">library</span>(enrichplot)<br></code></pre></td></tr></table></figure>
    277. 

  277. 

  278. <figure class="highlight stylus"><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 stylus"><br>kegg<span class="hljs-selector-class">.u2</span> &lt;- <span class="hljs-built_in">pairwise_termsim</span>(kegg.u)<br><span class="hljs-function"><span class="hljs-title">emapplot</span><span class="hljs-params">(kegg.u2,showCategory=<span class="hljs-number">15</span>)</span></span> <br><br>GO<span class="hljs-selector-class">.U</span><span class="hljs-selector-class">.MF2</span> &lt;- <span class="hljs-built_in">pairwise_termsim</span>(GO<span class="hljs-selector-class">.U</span>.MF)<br><span class="hljs-function"><span class="hljs-title">emapplot</span><span class="hljs-params">(GO.U.MF2,showCategory=<span class="hljs-number">15</span>)</span></span> <br><br></code></pre></td></tr></table></figure>
    279. 

  279. 

  280. <p><a target="_blank" rel="noopener" href="https://img-cdn.limour.top/blog_wp/2021/10/kegg.ema_.png"><img src="https://img-cdn.limour.top/blog_wp/2021/10/kegg.ema_.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></a></p>
    281. 

  281. <h2 id="第六步-共同基因绘图"><a href="#第六步-共同基因绘图" class="headerlink" title="第六步 共同基因绘图"></a>第六步 共同基因绘图</h2><figure class="highlight stylus"><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 stylus">f_kegg_readable_1 &lt;- <span class="hljs-built_in">function</span>(Oj, <span class="hljs-attribute">columns</span>=<span class="hljs-string">&quot;SYMBOL&quot;</span>, keytype=<span class="hljs-string">&quot;ENTREZID&quot;</span>)&#123;<br>    ge &lt;- Oj@gene<br>    ge &lt;- <span class="hljs-built_in">select</span>(org<span class="hljs-selector-class">.Hs</span><span class="hljs-selector-class">.eg</span><span class="hljs-selector-class">.db</span>,keys=ge,<span class="hljs-attribute">columns</span>=columns, keytype=keytype)<br>    ge2sy &lt;- ge<span class="hljs-selector-attr">[[columns]</span>]<br>    <span class="hljs-built_in">names</span>(ge2sy) &lt;- ge<span class="hljs-selector-attr">[[keytype]</span>]<br>    Oj@gene2Symbol &lt;- ge2sy<br>    Oj<br>&#125;<br>f_kegg_readable_2 &lt;- <span class="hljs-built_in">function</span>(str, ge2sy)&#123;<br>    res &lt;- <span class="hljs-built_in">strsplit</span>(str, <span class="hljs-string">&#x27;/&#x27;</span>)<br>    <span class="hljs-built_in">paste</span>(<span class="hljs-built_in">unlist</span>(ge2sy<span class="hljs-selector-attr">[unlist(res)]</span>),sep = <span class="hljs-string">&#x27;&#x27;</span>, collapse=<span class="hljs-string">&quot;/&quot;</span>)<br>&#125;<br>f_kegg_readable &lt;- <span class="hljs-built_in">function</span>(Oj)&#123;<br>    res &lt;- <span class="hljs-built_in">f_kegg_readable_1</span>(Oj)<br>    kegg.u2@result<span class="hljs-variable">$geneID</span> &lt;- <span class="hljs-built_in">lapply</span>(kegg.u2@result<span class="hljs-variable">$geneID</span>, f_kegg_readable_2, Oj@gene2Symbol)<br>    kegg<span class="hljs-selector-class">.u2</span><br>&#125;<br></code></pre></td></tr></table></figure>
    282. 

  282. 

  283. <figure class="highlight stylus"><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 stylus"><span class="hljs-function"><span class="hljs-title">cnetplot</span><span class="hljs-params">(GO.U.BP2, foldChange= f_gse_fuck(usignificant_markers<span class="hljs-variable">$gene</span>,usignificant_markers<span class="hljs-variable">$avg_log2FC</span>, lc_order = F)</span></span>)<br><span class="hljs-function"><span class="hljs-title">cnetplot</span><span class="hljs-params">(GO.U.MF2, foldChange= f_gse_fuck(usignificant_markers<span class="hljs-variable">$gene</span>,usignificant_markers<span class="hljs-variable">$avg_log2FC</span>, lc_order = F)</span></span>)<br></code></pre></td></tr></table></figure>
    284. 

  284. 

  285. <figure class="highlight reasonml"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs reasonml">cnetplot(f<span class="hljs-constructor">_kegg_readable(<span class="hljs-params">kegg</span>.<span class="hljs-params">u2</span>)</span>, foldChange= f<span class="hljs-constructor">_gse_fuck(<span class="hljs-params">usignificant_markers$gene</span>,<span class="hljs-params">usignificant_markers$avg_log2FC</span>, <span class="hljs-params">lc_order</span> = F)</span>)<br></code></pre></td></tr></table></figure>
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  646.   <script>Fluid.plugins.codeWidget();</script>
    647. 

  647. 

  648. 

  649.   
    650. 

  650. <script>
    651. 

  651.   Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
    652. 

  652.     window.anchors.options = {
    653. 

  653.       placement: CONFIG.anchorjs.placement,
    654. 

  654.       visible  : CONFIG.anchorjs.visible
    655. 

  655.     };
    656. 

  656.     if (CONFIG.anchorjs.icon) {
    657. 

  657.       window.anchors.options.icon = CONFIG.anchorjs.icon;
    658. 

  658.     }
    659. 

  659.     var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
    660. 

  660.     var res = [];
    661. 

  661.     for (var item of el) {
    662. 

  662.       res.push('.markdown-body > ' + item.trim());
    663. 

  663.     }
    664. 

  664.     if (CONFIG.anchorjs.placement === 'left') {
    665. 

  665.       window.anchors.options.class = 'anchorjs-link-left';
    666. 

  666.     }
    667. 

  667.     window.anchors.add(res.join(', '));
    668. 

  668. 

  669.     Fluid.events.registerRefreshCallback(function() {
    670. 

  670.       if ('anchors' in window) {
    671. 

  671.         anchors.removeAll();
    672. 

  672.         var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
    673. 

  673.         var res = [];
    674. 

  674.         for (var item of el) {
    675. 

  675.           res.push('.markdown-body > ' + item.trim());
    676. 

  676.         }
    677. 

  677.         if (CONFIG.anchorjs.placement === 'left') {
    678. 

  678.           anchors.options.class = 'anchorjs-link-left';
    679. 

  679.         }
    680. 

  680.         anchors.add(res.join(', '));
    681. 

  681.       }
    682. 

  682.     });
    683. 

  683.   });
    684. 

  684. </script>
    685. 

  685. 

  686. 

  687.   
    688. 

  688. <script>
    689. 

  689.   Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
    690. 

  690.     Fluid.plugins.fancyBox();
    691. 

  691.   });
    692. 

  692. </script>
    693. 

  693. 

  694. 

  695.   <script>Fluid.plugins.imageCaption();</script>
    696. 

  696. 

  697.   <script  src="/js/local-search.js" ></script>
    698. 

  698. 

  699. 

  700. 

  701. 

  702. 

  703. <!-- 主题的启动项，将它保持在最底部 -->
    704. 

  704. <!-- the boot of the theme, keep it at the bottom -->
    705. 

  705. <script  src="/js/boot.js" ></script>
    706. 

  706. 

  707. 

  708.   
    709. 

  709. 

  710.   <noscript>
    711. 

  711.     <div class="noscript-warning">Blog works best with JavaScript enabled</div>
    712. 

  712.   </noscript>
    713. 

  713. <!-- hexo injector body_end start -->
    714. 

  714.   <script defer src="/theme-inject/timeliness.js"></script>
    715. 

  715. <!-- hexo injector body_end end --></body>
    716. 

  716. </html>
    717.