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            <h1 id="seo-header">cellchat (四) 细胞间通讯分析</h1>
            
            
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                <h2 id="信息流分析"><a href="#信息流分析" class="headerlink" title="信息流分析"></a>信息流分析</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><span class="line">13</span><br></pre></td><td class="code"><pre><code class="hljs r">f_CC_IO_iN2pN <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> iN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    iN <span class="hljs-operator">&lt;-</span> gsub<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> iN<span class="hljs-punctuation">)</span><br>    unique<span class="hljs-punctuation">(</span>cellchat<span class="hljs-operator">@</span>DB<span class="hljs-operator">$</span>interaction<span class="hljs-punctuation">[</span>cellchat<span class="hljs-operator">@</span>DB<span class="hljs-operator">$</span>interaction<span class="hljs-operator">$</span>interaction_name_2 <span class="hljs-operator">%in%</span> iN<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;pathway_name&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>ComplexHeatmap<span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling  <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">,</span> pattern<span class="hljs-operator">=</span><span class="hljs-string">&#x27;all&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&quot;OrRd&quot;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">5</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> s_pathway<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    i <span class="hljs-operator">=</span> <span class="hljs-number">1</span><br>    pathway.union <span class="hljs-operator">&lt;-</span> union<span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">@</span>netP<span class="hljs-operator">$</span>pathways<span class="hljs-punctuation">,</span> object.list<span class="hljs-punctuation">[[</span>i<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">@</span>netP<span class="hljs-operator">$</span>pathways<span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>s_pathway<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>pathway.union <span class="hljs-operator">&lt;-</span> intersect<span class="hljs-punctuation">(</span>pathway.union<span class="hljs-punctuation">,</span> s_pathway<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br>    ht1 <span class="hljs-operator">=</span> netAnalysis_signalingRole_heatmap<span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> pattern<span class="hljs-punctuation">,</span> signaling <span class="hljs-operator">=</span> pathway.union<span class="hljs-punctuation">,</span> title <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">]</span><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> color.heatmap <span class="hljs-operator">=</span> color.heatmap<span class="hljs-punctuation">)</span><br>    ht2 <span class="hljs-operator">=</span> netAnalysis_signalingRole_heatmap<span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">[[</span>i<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> pattern<span class="hljs-punctuation">,</span> signaling <span class="hljs-operator">=</span> pathway.union<span class="hljs-punctuation">,</span> title <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>i<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><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> color.heatmap <span class="hljs-operator">=</span> color.heatmap<span class="hljs-punctuation">)</span><br>    draw<span class="hljs-punctuation">(</span>ht1 <span class="hljs-operator">+</span> ht2<span class="hljs-punctuation">,</span> ht_gap <span class="hljs-operator">=</span> unit<span class="hljs-punctuation">(</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;cm&quot;</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>

<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></pre></td><td class="code"><pre><code class="hljs r">SS_s_p <span class="hljs-operator">&lt;-</span> unlist<span class="hljs-punctuation">(</span>openxlsx<span class="hljs-operator">::</span>read.xlsx<span class="hljs-punctuation">(</span>xlsxFile <span class="hljs-operator">=</span> <span class="hljs-string">&quot;SS_selected_signaling_fibroblasts.xlsx&quot;</span><span class="hljs-punctuation">,</span> sheet <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> colNames <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>ER_s_p <span class="hljs-operator">&lt;-</span> unlist<span class="hljs-punctuation">(</span>openxlsx<span class="hljs-operator">::</span>read.xlsx<span class="hljs-punctuation">(</span>xlsxFile <span class="hljs-operator">=</span> <span class="hljs-string">&quot;ER_selected_signaling_fibroblasts.xlsx&quot;</span><span class="hljs-punctuation">,</span> sheet <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> colNames <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>CC_s_p <span class="hljs-operator">&lt;-</span> unlist<span class="hljs-punctuation">(</span>openxlsx<span class="hljs-operator">::</span>read.xlsx<span class="hljs-punctuation">(</span>xlsxFile <span class="hljs-operator">=</span> <span class="hljs-string">&quot;CC_selected_signaling_fibroblasts.xlsx&quot;</span><span class="hljs-punctuation">,</span> sheet <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> colNames <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;IO_signaling_all.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">8</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</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">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> xpd<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>SS_H<span class="hljs-punctuation">,</span> SS_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>ER_H<span class="hljs-punctuation">,</span> ER_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>CC_H<span class="hljs-punctuation">,</span> CC_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;IO_signaling_outgoing.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">8</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</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">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> xpd<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;outgoing&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;BuGn&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>SS_H<span class="hljs-punctuation">,</span> SS_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;outgoing&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;BuGn&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>ER_H<span class="hljs-punctuation">,</span> ER_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;outgoing&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;BuGn&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>CC_H<span class="hljs-punctuation">,</span> CC_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;IO_signaling_incoming.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">8</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</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">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> xpd<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;incoming&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;GnBu&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>SS_H<span class="hljs-punctuation">,</span> SS_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;incoming&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;GnBu&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>ER_H<span class="hljs-punctuation">,</span> ER_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_IO_signaling<span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;incoming&#x27;</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;GnBu&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">10</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> f_CC_IO_iN2pN<span class="hljs-punctuation">(</span>CC_H<span class="hljs-punctuation">,</span> CC_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="功能失调信号"><a href="#功能失调信号" class="headerlink" title="功能失调信号"></a>功能失调信号</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><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_CC_cmp_dysfunctional_signaling  <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> pos.dataset <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;CRPC&#x27;</span><span class="hljs-punctuation">,</span> neg.dataset<span class="hljs-operator">=</span><span class="hljs-string">&#x27;HSPC&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-comment"># define a char name used for storing the results of differential expression analysis</span><br>    features.name <span class="hljs-operator">=</span> pos.dataset<br>    <span class="hljs-comment"># perform differential expression analysis</span><br>    cellchat <span class="hljs-operator">&lt;-</span> identifyOverExpressedGenes<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> group.dataset <span class="hljs-operator">=</span> <span class="hljs-string">&quot;datasets&quot;</span><span class="hljs-punctuation">,</span> pos.dataset <span class="hljs-operator">=</span> pos.dataset<span class="hljs-punctuation">,</span> features.name <span class="hljs-operator">=</span> features.name<span class="hljs-punctuation">,</span> only.pos <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> thresh.pc <span class="hljs-operator">=</span> <span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span> thresh.fc <span class="hljs-operator">=</span> <span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span> thresh.p <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment">#&gt; Use the joint cell labels from the merged CellChat object</span><br>    <span class="hljs-comment"># map the results of differential expression analysis onto the inferred cell-cell communications to easily manage/subset the ligand-receptor pairs of interest</span><br>    net <span class="hljs-operator">&lt;-</span> netMappingDEG<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> features.name <span class="hljs-operator">=</span> features.name<span class="hljs-punctuation">)</span><br>    <span class="hljs-comment"># extract the ligand-receptor pairs with upregulated ligands in LS</span><br>    net.up <span class="hljs-operator">&lt;-</span> subsetCommunication<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> net <span class="hljs-operator">=</span> net<span class="hljs-punctuation">,</span> datasets <span class="hljs-operator">=</span> pos.dataset<span class="hljs-punctuation">,</span>ligand.logFC <span class="hljs-operator">=</span> <span class="hljs-number">0.2</span><span class="hljs-punctuation">,</span> receptor.logFC <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment"># extract the ligand-receptor pairs with upregulated ligands and upregulated recetptors in NL, i.e.,downregulated in LS</span><br>    net.down <span class="hljs-operator">&lt;-</span> subsetCommunication<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> net <span class="hljs-operator">=</span> net<span class="hljs-punctuation">,</span> datasets <span class="hljs-operator">=</span> neg.dataset<span class="hljs-punctuation">,</span>ligand.logFC <span class="hljs-operator">=</span> <span class="hljs-operator">-</span><span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span> receptor.logFC <span class="hljs-operator">=</span> <span class="hljs-operator">-</span><span class="hljs-number">0.1</span><span class="hljs-punctuation">)</span><br>    gene.up <span class="hljs-operator">&lt;-</span> extractGeneSubsetFromPair<span class="hljs-punctuation">(</span>net.up<span class="hljs-punctuation">,</span> cellchat<span class="hljs-punctuation">)</span><br>    gene.down <span class="hljs-operator">&lt;-</span> extractGeneSubsetFromPair<span class="hljs-punctuation">(</span>net.down<span class="hljs-punctuation">,</span> cellchat<span class="hljs-punctuation">)</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>net_up<span class="hljs-operator">=</span>net.up<span class="hljs-punctuation">,</span> net_down<span class="hljs-operator">=</span>net.down<span class="hljs-punctuation">,</span> gene_up<span class="hljs-operator">=</span>gene.up<span class="hljs-punctuation">,</span> gene_down<span class="hljs-operator">=</span>gene.down<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></pre></td><td class="code"><pre><code class="hljs r">dSS <span class="hljs-operator">&lt;-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">)</span><br>dER <span class="hljs-operator">&lt;-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">)</span><br>dCC <span class="hljs-operator">&lt;-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>CC<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><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></pre></td><td class="code"><pre><code class="hljs r">f_CC_s_p_intersect <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>net_info<span class="hljs-punctuation">,</span> DB_s_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    DB_s_p <span class="hljs-operator">&lt;-</span> gsub<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> DB_s_p<span class="hljs-punctuation">)</span><br>    DB_s_p <span class="hljs-operator">&lt;-</span> DB_s_p<span class="hljs-punctuation">[</span>DB_s_p <span class="hljs-operator">%in%</span> net_info<span class="hljs-operator">$</span>interaction_name_2<span class="hljs-punctuation">]</span><br>    net_info <span class="hljs-operator">&lt;-</span> net_info<span class="hljs-punctuation">[</span>net_info<span class="hljs-operator">$</span>interaction_name_2 <span class="hljs-operator">%in%</span> DB_s_p<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;interaction_name&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;interaction_name_2&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> drop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">]</span><br>    net_info <span class="hljs-operator">&lt;-</span> net_info<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;interaction_name&quot;</span><span class="hljs-punctuation">,</span> drop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">]</span><br>    net_info<br><span class="hljs-punctuation">&#125;</span><br>f_CC_cmp_dysfunctional_signaling_draw <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> f_res<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> sources.use<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> targets.use<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> pos.dataset <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;CRPC&#x27;</span><span class="hljs-punctuation">,</span> neg.dataset<span class="hljs-operator">=</span><span class="hljs-string">&#x27;HSPC&#x27;</span><span class="hljs-punctuation">,</span> pairLR.use.up<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> pairLR.use.down<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><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">is.null</span><span class="hljs-punctuation">(</span>f_res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        f_res <span class="hljs-operator">&lt;-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> pos.dataset <span class="hljs-operator">=</span> pos.dataset<span class="hljs-punctuation">,</span> neg.dataset <span class="hljs-operator">=</span> neg.dataset<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>targets.use<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        targets.use  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>cellchat<span class="hljs-operator">@</span>meta<span class="hljs-operator">$</span>ident<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>sources.use<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        sources.use  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>cellchat<span class="hljs-operator">@</span>meta<span class="hljs-operator">$</span>ident<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">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>pairLR.use.up<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        pairLR.use.up <span class="hljs-operator">=</span> f_res<span class="hljs-operator">$</span>net_up<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;interaction_name&quot;</span><span class="hljs-punctuation">,</span> drop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        pairLR.use.up <span class="hljs-operator">&lt;-</span> f_CC_s_p_intersect<span class="hljs-punctuation">(</span>f_res<span class="hljs-operator">$</span>net_up<span class="hljs-punctuation">,</span> pairLR.use.up<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    gg1 <span class="hljs-operator">&lt;-</span> netVisual_bubble<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> pairLR.use <span class="hljs-operator">=</span> pairLR.use.up<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> sources.use<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> targets.use<span class="hljs-punctuation">,</span> comparison <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">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>  angle.x <span class="hljs-operator">=</span> <span class="hljs-number">90</span><span class="hljs-punctuation">,</span> remove.isolate <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>title.name <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Up-regulated signaling in &quot;</span><span class="hljs-punctuation">,</span> pos.dataset<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment">#&gt; Comparing communications on a merged object</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>pairLR.use.down<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        pairLR.use.down <span class="hljs-operator">=</span> f_res<span class="hljs-operator">$</span>net_down<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;interaction_name&quot;</span><span class="hljs-punctuation">,</span> drop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        pairLR.use.down <span class="hljs-operator">&lt;-</span> f_CC_s_p_intersect<span class="hljs-punctuation">(</span>f_res<span class="hljs-operator">$</span>net_down<span class="hljs-punctuation">,</span> pairLR.use.down<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    gg2 <span class="hljs-operator">&lt;-</span> netVisual_bubble<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> pairLR.use <span class="hljs-operator">=</span> pairLR.use.down<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> sources.use<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> targets.use<span class="hljs-punctuation">,</span> comparison <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">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>  angle.x <span class="hljs-operator">=</span> <span class="hljs-number">90</span><span class="hljs-punctuation">,</span> remove.isolate <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span>title.name <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Down-regulated signaling in &quot;</span><span class="hljs-punctuation">,</span> pos.dataset<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment">#&gt; Comparing communications on a merged object</span><br>    gg1 <span class="hljs-operator">+</span> gg2<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></pre></td><td class="code"><pre><code class="hljs r">flt <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;TAM&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Mast&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;S100A8+ monocytes&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Proliferating T&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Proliferating Myeloid&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Luminal&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Endothelial&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Basal cell&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cDC2&#x27;</span><span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;dysfunctional_signaling.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</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">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> xpd<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">,</span> f_res <span class="hljs-operator">=</span> dSS<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> pairLR.use.up <span class="hljs-operator">=</span> SS_s_p<span class="hljs-punctuation">,</span> pairLR.use.down <span class="hljs-operator">=</span> SS_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">,</span> f_res <span class="hljs-operator">=</span> dER<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> pairLR.use.up <span class="hljs-operator">=</span> ER_s_p<span class="hljs-punctuation">,</span> pairLR.use.down <span class="hljs-operator">=</span> ER_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>CC<span class="hljs-punctuation">,</span> f_res <span class="hljs-operator">=</span> dCC<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> pairLR.use.up <span class="hljs-operator">=</span> CC_s_p<span class="hljs-punctuation">,</span> pairLR.use.down <span class="hljs-operator">=</span> CC_s_p<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;dysfunctional_signaling_t.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</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">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> xpd<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">,</span> f_res <span class="hljs-operator">=</span> dSS<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> pairLR.use.up <span class="hljs-operator">=</span> SS_s_p<span class="hljs-punctuation">,</span> pairLR.use.down <span class="hljs-operator">=</span> SS_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">,</span> f_res <span class="hljs-operator">=</span> dER<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> pairLR.use.up <span class="hljs-operator">=</span> ER_s_p<span class="hljs-punctuation">,</span> pairLR.use.down <span class="hljs-operator">=</span> ER_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>CC<span class="hljs-punctuation">,</span> f_res <span class="hljs-operator">=</span> dCC<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> pairLR.use.up <span class="hljs-operator">=</span> CC_s_p<span class="hljs-punctuation">,</span> pairLR.use.down <span class="hljs-operator">=</span> CC_s_p<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="细胞通路弦图"><a href="#细胞通路弦图" class="headerlink" title="细胞通路弦图"></a>细胞通路弦图</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">f_CC_IO_iN2pN_2 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> iN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    iN <span class="hljs-operator">&lt;-</span> gsub<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> iN<span class="hljs-punctuation">)</span><br>    unique<span class="hljs-punctuation">(</span>cellchat<span class="hljs-operator">@</span>DB<span class="hljs-operator">$</span>interaction<span class="hljs-punctuation">[</span>cellchat<span class="hljs-operator">@</span>DB<span class="hljs-operator">$</span>interaction<span class="hljs-operator">$</span>interaction_name_2 <span class="hljs-operator">%in%</span> iN<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pathway_name&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;interaction_name_2&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span><span class="hljs-string">&#x27;pathway_name&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_CC_cmp_nV_c_p  <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">,</span> sources.use<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> targets.use<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> s_pathway<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> title.name<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><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><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">)</span><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-operator">!</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>s_pathway<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            lc_pairLR.use <span class="hljs-operator">&lt;-</span> f_CC_IO_iN2pN_2<span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> s_pathway<span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span>lc_pairLR.use <span class="hljs-operator">=</span> s_pathway<span class="hljs-punctuation">&#125;</span><br>        try<span class="hljs-punctuation">(</span>netVisual_chord_gene<span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> sources.use<span class="hljs-punctuation">,</span> pairLR.use <span class="hljs-operator">=</span> lc_pairLR.use<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> targets.use<span class="hljs-punctuation">,</span> slot.name <span class="hljs-operator">=</span> <span class="hljs-string">&quot;netP&quot;</span><span class="hljs-punctuation">,</span> title.name <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Signaling pathways - &quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> legend.pos.x <span class="hljs-operator">=</span> <span class="hljs-number">10</span><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></pre></td><td class="code"><pre><code class="hljs r">pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;nV_c_p.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_nV_c_p<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> SS_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_nV_c_p<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> ER_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_nV_c_p<span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> CC_s_p<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;nV_c_p_t.pdf&#x27;</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_nV_c_p<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> SS_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_nV_c_p<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> ER_s_p<span class="hljs-punctuation">)</span><br>f_CC_cmp_nV_c_p<span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">,</span> targets.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Fibroblasts&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sources.use <span class="hljs-operator">=</span> flt<span class="hljs-punctuation">,</span> s_pathway <span class="hljs-operator">=</span> CC_s_p<span class="hljs-punctuation">)</span><br>dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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