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- <h1 id="seo-header">cellchat (二) 细胞间通讯分析</h1>
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- <h2 id="前置文章"><a href="#前置文章" class="headerlink" title="前置文章"></a>前置文章</h2><p><a target="_blank" rel="noopener" href="https://limour.top/1070.html">cellchat (一) 细胞间通讯分析</a></p>
- <h2 id="第一步-合并数据"><a href="#第一步-合并数据" class="headerlink" title="第一步 合并数据"></a>第一步 合并数据</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><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br></pre></td><td class="code"><pre><code class="hljs r">library<span class="hljs-punctuation">(</span>CellChat<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>patchwork<span class="hljs-punctuation">)</span><br><br><span class="hljs-comment">#01</span><br>SS_H <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'SS_H.rds'</span><span class="hljs-punctuation">)</span><br>SS_C <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'SS_C.rds'</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment">#02</span><br>ER_H <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'ER_H.rds'</span><span class="hljs-punctuation">)</span><br>ER_C <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'ER_C.rds'</span><span class="hljs-punctuation">)</span><br><br><span class="hljs-comment">#03</span><br>CC_H <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'CC_H.rds'</span><span class="hljs-punctuation">)</span><br>CC_C <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'CC_C.rds'</span><span class="hljs-punctuation">)</span><br><br>SS_l <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>HSPC <span class="hljs-operator">=</span> SS_H<span class="hljs-punctuation">,</span> CRPC <span class="hljs-operator">=</span> SS_C<span class="hljs-punctuation">)</span><br>ER_l <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>HSPC <span class="hljs-operator">=</span> ER_H<span class="hljs-punctuation">,</span> CRPC <span class="hljs-operator">=</span> ER_C<span class="hljs-punctuation">)</span><br>CC_l <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>HSPC <span class="hljs-operator">=</span> CC_H<span class="hljs-punctuation">,</span> CRPC <span class="hljs-operator">=</span> CC_C<span class="hljs-punctuation">)</span><br><br>SS <span class="hljs-operator"><-</span> mergeCellChat<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> add.names <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>ER <span class="hljs-operator"><-</span> mergeCellChat<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">,</span> add.names <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>CC <span class="hljs-operator"><-</span> mergeCellChat<span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">,</span> add.names <span class="hljs-operator">=</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>CC_l<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第二步-定义绘图函数"><a href="#第二步-定义绘图函数" class="headerlink" title="第二步 定义绘图函数"></a>第二步 定义绘图函数</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><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><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</span><br><span class="line">88</span><br><span class="line">89</span><br><span class="line">90</span><br><span class="line">91</span><br><span class="line">92</span><br><span class="line">93</span><br><span class="line">94</span><br><span class="line">95</span><br><span class="line">96</span><br><span class="line">97</span><br><span class="line">98</span><br></pre></td><td class="code"><pre><code class="hljs r">f_CC_cmp_nVheatmap <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> gg1 <span class="hljs-operator"><-</span> netVisual_heatmap<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Do heatmap based on a merged object</span><br> gg2 <span class="hljs-operator"><-</span> netVisual_heatmap<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> measure <span class="hljs-operator">=</span> <span class="hljs-string">"weight"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Do heatmap based on a merged object</span><br> gg1 <span class="hljs-operator">+</span> gg2<br><span class="hljs-punctuation">}</span><br><br>f_CC_cmp_major_sources_and_targets <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> num.link <span class="hljs-operator"><-</span> sapply<span class="hljs-punctuation">(</span>object.list<span class="hljs-punctuation">,</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">{</span>rowSums<span class="hljs-punctuation">(</span>x<span class="hljs-operator">@</span>net<span class="hljs-operator">$</span>count<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> colSums<span class="hljs-punctuation">(</span>x<span class="hljs-operator">@</span>net<span class="hljs-operator">$</span>count<span class="hljs-punctuation">)</span><span class="hljs-operator">-</span>diag<span class="hljs-punctuation">(</span>x<span class="hljs-operator">@</span>net<span class="hljs-operator">$</span>count<span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><br> weight.MinMax <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">min</span><span class="hljs-punctuation">(</span>num.link<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">max</span><span class="hljs-punctuation">(</span>num.link<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># control the dot size in the different datasets</span><br> gg <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>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">{</span><br> gg<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> netAnalysis_signalingRole_scatter<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> 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> weight.MinMax <span class="hljs-operator">=</span> weight.MinMax<span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-comment">#> Signaling role analysis on the aggregated cell-cell communication network from all signaling pathways</span><br> <span class="hljs-comment">#> Signaling role analysis on the aggregated cell-cell communication network from all signaling pathways</span><br> print<span class="hljs-punctuation">(</span>patchwork<span class="hljs-operator">::</span>wrap_plots<span class="hljs-punctuation">(</span>plots <span class="hljs-operator">=</span> gg<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br><br>f_CC_cmp_SG_F <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> cellchat <span class="hljs-operator"><-</span> computeNetSimilarityPairwise<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"functional"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Compute signaling network similarity for datasets 1 2</span><br> cellchat <span class="hljs-operator"><-</span> netEmbedding<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"functional"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Manifold learning of the signaling networks for datasets 1 2</span><br> cellchat <span class="hljs-operator"><-</span> netClustering<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"functional"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Classification learning of the signaling networks for datasets 1 2</span><br> <span class="hljs-comment"># Visualization in 2D-space</span><br> netVisual_embeddingPairwise<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"functional"</span><span class="hljs-punctuation">,</span> label.size <span class="hljs-operator">=</span> <span class="hljs-number">3.5</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> 2D visualization of signaling networks from datasets 1 2</span><br><span class="hljs-punctuation">}</span><br><br>f_CC_cmp_SG_S <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> cellchat <span class="hljs-operator"><-</span> computeNetSimilarityPairwise<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"structural"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Compute signaling network similarity for datasets 1 2</span><br> cellchat <span class="hljs-operator"><-</span> netEmbedding<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"structural"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Manifold learning of the signaling networks for datasets 1 2</span><br> cellchat <span class="hljs-operator"><-</span> netClustering<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"structural"</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Classification learning of the signaling networks for datasets 1 2</span><br> <span class="hljs-comment"># Visualization in 2D-space</span><br> netVisual_embeddingPairwise<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> type <span class="hljs-operator">=</span> <span class="hljs-string">"structural"</span><span class="hljs-punctuation">,</span> label.size <span class="hljs-operator">=</span> <span class="hljs-number">3.5</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> 2D visualization of signaling networks from datasets 1 2</span><br><span class="hljs-punctuation">}</span><br><br>f_CC_cmp_overall_information_flow <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> gg1 <span class="hljs-operator"><-</span> rankNet<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> mode <span class="hljs-operator">=</span> <span class="hljs-string">"comparison"</span><span class="hljs-punctuation">,</span> stacked <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> do.stat <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br> gg2 <span class="hljs-operator"><-</span> rankNet<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> mode <span class="hljs-operator">=</span> <span class="hljs-string">"comparison"</span><span class="hljs-punctuation">,</span> stacked <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> do.stat <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br> gg1 <span class="hljs-operator">+</span> gg2<br><span class="hljs-punctuation">}</span><br><br>f_CC_cmp_IO_signaling <span class="hljs-operator"><-</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">'all'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">"OrRd"</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><span class="hljs-punctuation">{</span><br> i <span class="hljs-operator">=</span> <span class="hljs-number">1</span><br> <span class="hljs-comment"># combining all the identified signaling pathways from different datasets </span><br> pathway.union <span class="hljs-operator"><-</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> 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">"cm"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br><br>f_CC_cmp_dysfunctional_signaling <span class="hljs-operator"><-</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">'CRPC'</span><span class="hljs-punctuation">,</span> neg.dataset<span class="hljs-operator">=</span><span class="hljs-string">'HSPC'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</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"><-</span> identifyOverExpressedGenes<span class="hljs-punctuation">(</span>cellchat<span class="hljs-punctuation">,</span> group.dataset <span class="hljs-operator">=</span> <span class="hljs-string">"datasets"</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">#> 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"><-</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"><-</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"><-</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"><-</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"><-</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">}</span><br><br>f_CC_cmp_dysfunctional_signaling_draw <span class="hljs-operator"><-</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">'CRPC'</span><span class="hljs-punctuation">,</span> neg.dataset<span class="hljs-operator">=</span><span class="hljs-string">'HSPC'</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">{</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">{</span><br> f_res <span class="hljs-operator"><-</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">}</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">{</span><br> targets.use <span class="hljs-operator"><-</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">}</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">{</span><br> sources.use <span class="hljs-operator"><-</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">$</span>ident<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>pairLR.use.up<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> pairLR.use.up <span class="hljs-operator">=</span> f_res<span class="hljs-operator">$</span>net_up<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-string">"interaction_name"</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">}</span><br> gg1 <span class="hljs-operator"><-</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">"Up-regulated signaling in "</span><span class="hljs-punctuation">,</span> pos.dataset<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> 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">{</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">"interaction_name"</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">}</span><br> gg2 <span class="hljs-operator"><-</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">"Down-regulated signaling in "</span><span class="hljs-punctuation">,</span> pos.dataset<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-comment">#> Comparing communications on a merged object</span><br> gg1 <span class="hljs-operator">+</span> gg2<br><span class="hljs-punctuation">}</span><br></code></pre></td></tr></table></figure>
- <h2 id="第三步-绘图"><a href="#第三步-绘图" class="headerlink" title="第三步 绘图"></a>第三步 绘图</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><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><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</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">'nVheatmap.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</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_nVheatmap<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">)</span><br>f_CC_cmp_nVheatmap<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">)</span><br>f_CC_cmp_nVheatmap<span class="hljs-punctuation">(</span>CC<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">'major_sources_and_targets.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</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_major_sources_and_targets<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">)</span><br>f_CC_cmp_major_sources_and_targets<span class="hljs-punctuation">(</span>ER_l<span class="hljs-punctuation">)</span><br>f_CC_cmp_major_sources_and_targets<span class="hljs-punctuation">(</span>CC_l<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">'SG_F.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</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_SG_F<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">)</span><br>f_CC_cmp_SG_F<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">)</span><br>f_CC_cmp_SG_F<span class="hljs-punctuation">(</span>CC<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">'SG_S.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</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_SG_S<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">)</span><br>f_CC_cmp_SG_S<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">)</span><br>f_CC_cmp_SG_S<span class="hljs-punctuation">(</span>CC<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">'overall_information_flow.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</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_overall_information_flow<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">)</span><br>f_CC_cmp_overall_information_flow<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">)</span><br>f_CC_cmp_overall_information_flow<span class="hljs-punctuation">(</span>CC<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">'IO_signaling_all.pdf'</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_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">24</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">24</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">24</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">'IO_signaling_outgoing.pdf'</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_IO_signaling<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">'outgoing'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">'BuGn'</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">24</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">'outgoing'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">'BuGn'</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">24</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">'outgoing'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">'BuGn'</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">24</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">'IO_signaling_incoming.pdf'</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_IO_signaling<span class="hljs-punctuation">(</span>SS_l<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">'incoming'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">'GnBu'</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">24</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">'incoming'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">'GnBu'</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">24</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">'incoming'</span><span class="hljs-punctuation">,</span> color.heatmap <span class="hljs-operator">=</span> <span class="hljs-string">'GnBu'</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">24</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">'dysfunctional_signaling.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">24</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> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'Fibroblasts'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>ER<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">'Fibroblasts'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>CC<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">'Fibroblasts'</span><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">'dysfunctional_signaling_TAM.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">24</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> sources.use <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'TAM'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>ER<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">'TAM'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_CC_cmp_dysfunctional_signaling_draw<span class="hljs-punctuation">(</span>CC<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">'TAM'</span><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>tss <span class="hljs-operator"><-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>SS<span class="hljs-punctuation">)</span><br>ter <span class="hljs-operator"><-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>ER<span class="hljs-punctuation">)</span><br>tcc <span class="hljs-operator"><-</span> f_CC_cmp_dysfunctional_signaling<span class="hljs-punctuation">(</span>CC<span class="hljs-punctuation">)</span><br><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">'dysfunctional_signaling_TAM_t.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">24</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> tss<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">'TAM'</span><span class="hljs-punctuation">)</span><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> ter<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">'TAM'</span><span class="hljs-punctuation">)</span><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> tcc<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">'TAM'</span><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">'dysfunctional_signaling_t.pdf'</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">24</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> tss<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">'Fibroblasts'</span><span class="hljs-punctuation">)</span><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> ter<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">'Fibroblasts'</span><span class="hljs-punctuation">)</span><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> tcc<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">'Fibroblasts'</span><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>
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