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- <h1 id="seo-header">scMetabolism分析细胞代谢</h1>
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- <h2 id="包安装"><a href="#包安装" class="headerlink" title="包安装"></a>包安装</h2><p><a target="_blank" rel="noopener" href="https://github.com/wu-yc/scMetabolism">https://github.com/wu-yc/scMetabolism</a></p>
- <h2 id="第一步-分离对比对象"><a href="#第一步-分离对比对象" class="headerlink" title="第一步 分离对比对象"></a>第一步 分离对比对象</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></pre></td><td class="code"><pre><code class="hljs r">HSPC <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">,</span> group <span class="hljs-operator">==</span> <span class="hljs-string">'HSPC'</span><span class="hljs-punctuation">)</span><br>CPRC <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">,</span> group <span class="hljs-operator">==</span> <span class="hljs-string">'CRPC'</span><span class="hljs-punctuation">)</span><br>countexp_HSPC <span class="hljs-operator"><-</span>sc.metabolism.Seurat<span class="hljs-punctuation">(</span>obj <span class="hljs-operator">=</span> HSPC<span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">"VISION"</span><span class="hljs-punctuation">,</span> imputation <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> ncores <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> metabolism.type <span class="hljs-operator">=</span> <span class="hljs-string">"KEGG"</span><span class="hljs-punctuation">)</span><br>countexp_CPRC <span class="hljs-operator"><-</span>sc.metabolism.Seurat<span class="hljs-punctuation">(</span>obj <span class="hljs-operator">=</span> CPRC<span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">"VISION"</span><span class="hljs-punctuation">,</span> imputation <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> ncores <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> metabolism.type <span class="hljs-operator">=</span> <span class="hljs-string">"KEGG"</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第二步-获得代谢矩阵"><a href="#第二步-获得代谢矩阵" class="headerlink" title="第二步 获得代谢矩阵"></a>第二步 获得代谢矩阵</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs r">etabolism.matrix_HSPC <span class="hljs-operator"><-</span> countexp_HSPC<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<br>etabolism.matrix_CPRC <span class="hljs-operator"><-</span> countexp_CPRC<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<br></code></pre></td></tr></table></figure>
- <h2 id="第三步-代谢差异分析"><a href="#第三步-代谢差异分析" class="headerlink" title="第三步 代谢差异分析"></a>第三步 代谢差异分析</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><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></pre></td><td class="code"><pre><code class="hljs r">f_DEmetabolism_01 <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">,</span> matrixE<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> rownames<span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> res<span class="hljs-punctuation">[[</span><span class="hljs-string">'meanN'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br> res<span class="hljs-punctuation">[[</span><span class="hljs-string">'meanE'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br> res<span class="hljs-punctuation">[[</span><span class="hljs-string">'p-value'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">1</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nrow<span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> test <span class="hljs-operator"><-</span> t.test<span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>unlist<span class="hljs-punctuation">(</span>matrixE<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> res<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span> <span class="hljs-string">'p-value'</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> test<span class="hljs-operator">$</span>p.value<br> res<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span> <span class="hljs-string">'meanN'</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> test<span class="hljs-operator">$</span>estimate<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br> res<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span> <span class="hljs-string">'meanE'</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> test<span class="hljs-operator">$</span>estimate<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">}</span><br> res<span class="hljs-punctuation">[[</span><span class="hljs-string">'def'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> with<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> meanE <span class="hljs-operator">-</span> meanN<span class="hljs-punctuation">)</span><br> res<br><span class="hljs-punctuation">}</span><br>f_metaN2cellN <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">,</span> matrixN<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> idx <span class="hljs-operator"><-</span> which<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">==</span> typeN<span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>gsub<span class="hljs-punctuation">(</span><span class="hljs-string">'-'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'.'</span><span class="hljs-punctuation">,</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>idx<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">{</span><br> <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>idx<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br><span class="hljs-punctuation">}</span><br>f_DEmetabolism <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>countexpN<span class="hljs-punctuation">,</span> countexpE<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> matrixN <span class="hljs-operator"><-</span> countexpN<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<br> matrixE <span class="hljs-operator"><-</span> countexpE<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<br> matrixN <span class="hljs-operator"><-</span> matrixN<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_metaN2cellN<span class="hljs-punctuation">(</span>countexpN<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> matrixE <span class="hljs-operator"><-</span> matrixE<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_metaN2cellN<span class="hljs-punctuation">(</span>countexpE<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> f_DEmetabolism_01<span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">,</span> matrixE<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br></code></pre></td></tr></table></figure>
- <h2 id="第四步-代谢差异展示"><a href="#第四步-代谢差异展示" class="headerlink" title="第四步 代谢差异展示"></a>第四步 代谢差异展示</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></pre></td><td class="code"><pre><code class="hljs r">require<span class="hljs-punctuation">(</span>ggrepel<span class="hljs-punctuation">)</span><br>f_ggplot2_ti <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">,</span> title<span class="hljs-punctuation">,</span> subtitle<span class="hljs-operator">=</span><span class="hljs-string">''</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>subtitle <span class="hljs-operator">==</span> <span class="hljs-string">''</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-punctuation">(</span>p <span class="hljs-operator">+</span> ggtitle<span class="hljs-punctuation">(</span>title<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">{</span><br> <span class="hljs-punctuation">(</span>p <span class="hljs-operator">+</span> ggtitle<span class="hljs-punctuation">(</span>title<span class="hljs-punctuation">,</span> subtitle<span class="hljs-operator">=</span>subtitle<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <br> theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> plot.subtitle <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><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-punctuation">}</span><br>f_DEmetabolism_Volcano <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>countexpN<span class="hljs-punctuation">,</span> countexpE<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">,</span> delta <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> Threshold_p <span class="hljs-operator">=</span> <span class="hljs-number">0.05</span><span class="hljs-punctuation">,</span> lc_rep<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> DEmm <span class="hljs-operator"><-</span> f_DEmetabolism<span class="hljs-punctuation">(</span>countexpN<span class="hljs-punctuation">,</span> countexpE<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">)</span><br> col_vector <span class="hljs-operator">=</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>rgb<span class="hljs-punctuation">(</span><span class="hljs-number">108</span><span class="hljs-punctuation">,</span> <span class="hljs-number">200</span><span class="hljs-punctuation">,</span> <span class="hljs-number">228</span><span class="hljs-punctuation">,</span> maxColorValue <span class="hljs-operator">=</span> <span class="hljs-number">255</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> Threshold <span class="hljs-operator">=</span> with<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">,</span> delta<span class="hljs-operator">*</span>sd<span class="hljs-punctuation">(</span><span class="hljs-built_in">abs</span><span class="hljs-punctuation">(</span>def<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <br> col_vector<span class="hljs-punctuation">[</span>with<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">,</span> `p-value` <span class="hljs-operator"><</span> Threshold_p <span class="hljs-operator">&</span> def <span class="hljs-operator">></span> Threshold<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> rgb<span class="hljs-punctuation">(</span><span class="hljs-number">226</span><span class="hljs-punctuation">,</span> <span class="hljs-number">61</span><span class="hljs-punctuation">,</span> <span class="hljs-number">75</span><span class="hljs-punctuation">,</span> maxColorValue <span class="hljs-operator">=</span> <span class="hljs-number">255</span><span class="hljs-punctuation">)</span><br> col_vector<span class="hljs-punctuation">[</span>with<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">,</span> `p-value` <span class="hljs-operator"><</span> Threshold_p <span class="hljs-operator">&</span> def <span class="hljs-operator"><</span> <span class="hljs-operator">-</span>Threshold<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> rgb<span class="hljs-punctuation">(</span><span class="hljs-number">232</span><span class="hljs-punctuation">,</span> <span class="hljs-number">168</span><span class="hljs-punctuation">,</span> <span class="hljs-number">71</span><span class="hljs-punctuation">,</span> maxColorValue <span class="hljs-operator">=</span> <span class="hljs-number">255</span><span class="hljs-punctuation">)</span><br> <br> DEmm<span class="hljs-punctuation">[[</span><span class="hljs-string">'Name'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">)</span><br> DEmm<span class="hljs-punctuation">[[</span><span class="hljs-string">'col'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> col_vector<br> DEmm<span class="hljs-punctuation">[[</span><span class="hljs-string">'-log10(P)'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> with<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">,</span> <span class="hljs-operator">-</span>log10<span class="hljs-punctuation">(</span>`p-value`<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <br> lc_tp_logFC <span class="hljs-operator"><-</span> DEmm<span class="hljs-operator">$</span>def<br> lc_tp_logFC<span class="hljs-punctuation">[</span>with<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">,</span> `p-value` <span class="hljs-operator">>=</span> Threshold_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br> lc_idx <span class="hljs-operator"><-</span> order<span class="hljs-punctuation">(</span>lc_tp_logFC<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span>lc_rep<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">)</span><span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-operator">-</span>lc_rep<span class="hljs-punctuation">)</span><span class="hljs-operator">:</span>nrow<span class="hljs-punctuation">(</span>DEmm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> <br> res <span class="hljs-operator"><-</span> ggplot<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> geom_point<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>def<span class="hljs-punctuation">,</span> `-log10(P)`<span class="hljs-punctuation">,</span> col<span class="hljs-operator">=</span>I<span class="hljs-punctuation">(</span>col<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> DEmm<span class="hljs-punctuation">)</span> <br> res <span class="hljs-operator"><-</span> res <span class="hljs-operator">+</span> theme_bw<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>panel.grid<span class="hljs-operator">=</span>element_line<span class="hljs-punctuation">(</span>colour<span class="hljs-operator">=</span><span class="hljs-literal">NA</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> res <span class="hljs-operator">+</span> geom_hline<span class="hljs-punctuation">(</span>yintercept<span class="hljs-operator">=</span><span class="hljs-operator">-</span>log10<span class="hljs-punctuation">(</span>Threshold_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> linetype<span class="hljs-operator">=</span><span class="hljs-string">"longdash"</span><span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> res <span class="hljs-operator">+</span> geom_vline<span class="hljs-punctuation">(</span>xintercept<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>Threshold<span class="hljs-punctuation">,</span> <span class="hljs-operator">-</span>Threshold<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> linetype<span class="hljs-operator">=</span><span class="hljs-string">"longdash"</span><span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> res <span class="hljs-operator">+</span> geom_text_repel<span class="hljs-punctuation">(</span>data<span class="hljs-operator">=</span>DEmm<span class="hljs-punctuation">[</span>lc_idx<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>aes<span class="hljs-punctuation">(</span>def<span class="hljs-punctuation">,</span>`-log10(P)`<span class="hljs-punctuation">,</span>label<span class="hljs-operator">=</span>Name<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> force<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> max.overlaps<span class="hljs-operator">=</span><span class="hljs-literal">Inf</span><span class="hljs-punctuation">)</span><br> f_ggplot2_ti<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> typeN<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br></code></pre></td></tr></table></figure>
- <h2 id="第五步-全部展示"><a href="#第五步-全部展示" class="headerlink" title="第五步 全部展示"></a>第五步 全部展示</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></pre></td><td class="code"><pre><code class="hljs r">require<span class="hljs-punctuation">(</span>export<span class="hljs-punctuation">)</span><br>f_ppt_output <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>fileName<span class="hljs-punctuation">,</span> image<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>p <span class="hljs-keyword">in</span> image<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> graph2ppt<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>p<span class="hljs-punctuation">,</span> file<span class="hljs-operator">=</span>fileName<span class="hljs-punctuation">,</span> width<span class="hljs-operator">=</span><span class="hljs-number">9</span><span class="hljs-punctuation">,</span> aspectr<span class="hljs-operator">=</span><span class="hljs-number">1.5</span><span class="hljs-punctuation">,</span> append <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br><span class="hljs-punctuation">}</span><br>pl <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>tN <span class="hljs-keyword">in</span> unique<span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>countexp_HSPC<span class="hljs-punctuation">[[</span><span class="hljs-string">'immune_type_2'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> pl<span class="hljs-punctuation">[[</span>tN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> f_DEmetabolism_Volcano<span class="hljs-punctuation">(</span>countexp_HSPC<span class="hljs-punctuation">,</span> countexp_CPRC<span class="hljs-punctuation">,</span> <span class="hljs-string">'immune_type_2'</span><span class="hljs-punctuation">,</span> tN<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br>f_ppt_output<span class="hljs-punctuation">(</span><span class="hljs-string">'HSPC vs CRPC.pptx'</span><span class="hljs-punctuation">,</span> pl<span class="hljs-punctuation">)</span><br><br>input.pathway<span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>countexp_HSPC<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<span class="hljs-punctuation">)</span><br>p1 <span class="hljs-operator"><-</span> DotPlot.metabolism<span class="hljs-punctuation">(</span>obj <span class="hljs-operator">=</span> countexp_HSPC<span class="hljs-punctuation">,</span> pathway <span class="hljs-operator">=</span> input.pathway<span class="hljs-punctuation">,</span> phenotype <span class="hljs-operator">=</span> <span class="hljs-string">"immune_type_2"</span><span class="hljs-punctuation">,</span> norm <span class="hljs-operator">=</span> <span class="hljs-string">"y"</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> DotPlot.metabolism<span class="hljs-punctuation">(</span>obj <span class="hljs-operator">=</span> countexp_CPRC<span class="hljs-punctuation">,</span> pathway <span class="hljs-operator">=</span> input.pathway<span class="hljs-punctuation">,</span> phenotype <span class="hljs-operator">=</span> <span class="hljs-string">"immune_type_2"</span><span class="hljs-punctuation">,</span> norm <span class="hljs-operator">=</span> <span class="hljs-string">"y"</span><span class="hljs-punctuation">)</span><br>ggsave<span class="hljs-punctuation">(</span>p1<span class="hljs-punctuation">,</span> filename <span class="hljs-operator">=</span> <span class="hljs-string">'HSPC vs CRPC.pdf'</span><span class="hljs-punctuation">,</span> dpi <span class="hljs-operator">=</span> <span class="hljs-number">1200</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">36</span><span class="hljs-punctuation">,</span> device <span class="hljs-operator">=</span> <span class="hljs-string">'pdf'</span><span class="hljs-punctuation">,</span> limitsize <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第六步-基因热图-获取代谢相关基因"><a href="#第六步-基因热图-获取代谢相关基因" class="headerlink" title="第六步 基因热图-获取代谢相关基因"></a>第六步 基因热图-获取代谢相关基因</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><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></pre></td><td class="code"><pre><code class="hljs r">require<span class="hljs-punctuation">(</span>KEGGREST<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>stringr<span class="hljs-punctuation">)</span><br>f_KEGG_name2id <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>keggL<span class="hljs-punctuation">,</span> nameL<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> <span class="hljs-literal">NULL</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>nameL<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> fuck <span class="hljs-operator"><-</span> gsub<span class="hljs-punctuation">(</span>pattern <span class="hljs-operator">=</span> <span class="hljs-string">'\\('</span><span class="hljs-punctuation">,</span> replacement <span class="hljs-operator">=</span> <span class="hljs-string">'\\\\('</span><span class="hljs-punctuation">,</span> x <span class="hljs-operator">=</span> nameL<span class="hljs-punctuation">[[</span>i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> fuck <span class="hljs-operator"><-</span> gsub<span class="hljs-punctuation">(</span>pattern <span class="hljs-operator">=</span> <span class="hljs-string">'\\)'</span><span class="hljs-punctuation">,</span> replacement <span class="hljs-operator">=</span> <span class="hljs-string">'\\\\)'</span><span class="hljs-punctuation">,</span> x <span class="hljs-operator">=</span> fuck<span class="hljs-punctuation">)</span><br> idx <span class="hljs-operator"><-</span> str_detect<span class="hljs-punctuation">(</span>keggL<span class="hljs-punctuation">,</span> fuck<span class="hljs-punctuation">)</span><br> tmp <span class="hljs-operator"><-</span> keggL<span class="hljs-punctuation">[</span>idx<span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> tmp <span class="hljs-operator"><-</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br> tmp <span class="hljs-operator"><-</span> substr<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span>tmp<span class="hljs-punctuation">,</span> start <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> stop<span class="hljs-operator">=</span><span class="hljs-number">15</span><span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> tmp<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">length</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">></span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> print<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-punctuation">}</span><br> res<br><span class="hljs-punctuation">}</span><br>f_KEGG_id2symbol <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>KEGGid<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> <span class="hljs-literal">NULL</span><br> <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>hsa_id <span class="hljs-keyword">in</span> KEGGid<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> hsa_info <span class="hljs-operator"><-</span> keggGet<span class="hljs-punctuation">(</span>hsa_id<span class="hljs-punctuation">)</span><br> hsa_info <span class="hljs-operator"><-</span> hsa_info<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>GENE<br> hsa_info <span class="hljs-operator"><-</span> hsa_info<span class="hljs-punctuation">[</span>seq<span class="hljs-punctuation">(</span>from <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">,</span> to <span class="hljs-operator">=</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>hsa_info<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> by <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> hsa_info <span class="hljs-operator"><-</span> strsplit<span class="hljs-punctuation">(</span>hsa_info<span class="hljs-punctuation">,</span>split <span class="hljs-operator">=</span> <span class="hljs-string">';'</span><span class="hljs-punctuation">)</span><br> hsa_info <span class="hljs-operator"><-</span> unlist<span class="hljs-punctuation">(</span>lapply<span class="hljs-punctuation">(</span>hsa_info<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>X<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> hsa_info<span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> res <span class="hljs-operator"><-</span> unique<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> res<span class="hljs-punctuation">[</span>str_detect<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">'\\] \\['</span><span class="hljs-punctuation">,</span> negate <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> res<br><span class="hljs-punctuation">}</span><br>MMPath <span class="hljs-operator"><-</span> keggGet<span class="hljs-punctuation">(</span><span class="hljs-string">'hsa01100'</span><span class="hljs-punctuation">)</span><br>MMPath <span class="hljs-operator"><-</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>MMPath<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">$</span>REL_PATHWAY<span class="hljs-punctuation">)</span><br>MMgene <span class="hljs-operator"><-</span> f_KEGG_id2symbol<span class="hljs-punctuation">(</span>MMPath<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第六步-绘制基因热图"><a href="#第六步-绘制基因热图" class="headerlink" title="第六步 绘制基因热图"></a>第六步 绘制基因热图</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></pre></td><td class="code"><pre><code class="hljs r">f_metaG2G <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">,</span> matrixN<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br> alltype <span class="hljs-operator"><-</span> unique<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>type <span class="hljs-keyword">in</span> alltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">==</span> type<span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">'-'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'.'</span><span class="hljs-punctuation">,</span>res<span class="hljs-punctuation">[[</span>type<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-punctuation">}</span><br> res<br><span class="hljs-punctuation">}</span><br>f_matrix_groupMean <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>matrixA<span class="hljs-punctuation">,</span> group<span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> rownames<span class="hljs-punctuation">(</span>matrixA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> group <span class="hljs-operator"><-</span> f_metaG2G<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> matrixN<span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> rowMeans<span class="hljs-punctuation">(</span>matrixA<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>group<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> res<br><span class="hljs-punctuation">}</span><br>require<span class="hljs-punctuation">(</span>reshape2<span class="hljs-punctuation">)</span><br>f_matrix_heatmap <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-comment"># 标准化一下</span><br><span class="hljs-comment"># dfA <- as.data.frame(scale(dfA))</span><br> <span class="hljs-comment"># 转换前，先增加一列ID列，保存行名字</span><br> dfA<span class="hljs-operator">$</span>df_ID <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">)</span><br> dfm <span class="hljs-operator"><-</span> melt<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">,</span> na.rm <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> id.vars <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'df_ID'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> ggplot<span class="hljs-punctuation">(</span>dfm<span class="hljs-punctuation">,</span> aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>variable<span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span>df_ID<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> geom_tile<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>fill<span class="hljs-operator">=</span>value<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>angle<span class="hljs-operator">=</span><span class="hljs-number">45</span><span class="hljs-punctuation">,</span> hjust<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> vjust<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> scale_fill_gradient<span class="hljs-punctuation">(</span>low <span class="hljs-operator">=</span> <span class="hljs-string">"blue"</span><span class="hljs-punctuation">,</span> high <span class="hljs-operator">=</span> <span class="hljs-string">"pink"</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> xlab<span class="hljs-punctuation">(</span><span class="hljs-string">"samples"</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme_bw<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>panel.grid.major <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>legend.key<span class="hljs-operator">=</span>element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p<br><span class="hljs-punctuation">}</span><br><br>mono <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">,</span> immune_type_2 <span class="hljs-operator">%in%</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-string">'monocytes'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'S100A8+ monocytes'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>mono <span class="hljs-operator"><-</span> sc.metabolism.Seurat<span class="hljs-punctuation">(</span>obj <span class="hljs-operator">=</span> mono<span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">"VISION"</span><span class="hljs-punctuation">,</span> imputation <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> ncores <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> metabolism.type <span class="hljs-operator">=</span> <span class="hljs-string">"KEGG"</span><span class="hljs-punctuation">)</span><br>a <span class="hljs-operator"><-</span> f_matrix_groupMean<span class="hljs-punctuation">(</span>mono<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<span class="hljs-punctuation">,</span> mono<span class="hljs-punctuation">[[</span><span class="hljs-string">'patient_id'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>p <span class="hljs-operator"><-</span> f_matrix_heatmap<span class="hljs-punctuation">(</span>a<span class="hljs-punctuation">)</span><br>ggsave<span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">,</span> filename <span class="hljs-operator">=</span> <span class="hljs-string">'mono_HSPC vs CRPC_heatmap.pdf'</span><span class="hljs-punctuation">,</span> dpi <span class="hljs-operator">=</span> <span class="hljs-number">1200</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">8</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> device <span class="hljs-operator">=</span> <span class="hljs-string">'pdf'</span><span class="hljs-punctuation">,</span> limitsize <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第七步-绘制交叉热图"><a href="#第七步-绘制交叉热图" class="headerlink" title="第七步 绘制交叉热图"></a>第七步 绘制交叉热图</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></pre></td><td class="code"><pre><code class="hljs r">f_metaG2G <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">,</span> matrixN<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br> alltype <span class="hljs-operator"><-</span> unique<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>type <span class="hljs-keyword">in</span> alltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">==</span> type<span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">'-'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'.'</span><span class="hljs-punctuation">,</span>res<span class="hljs-punctuation">[[</span>type<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-punctuation">}</span><br> res<br><span class="hljs-punctuation">}</span><br>f_matrix_groupMean <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>matrixA<span class="hljs-punctuation">,</span> group<span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> rownames<span class="hljs-punctuation">(</span>matrixA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> group <span class="hljs-operator"><-</span> f_metaG2G<span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> matrixN<span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">)</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">length</span><span class="hljs-punctuation">(</span>group<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> matrixA<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>group<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">}</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> rowMeans<span class="hljs-punctuation">(</span>matrixA<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>group<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><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-punctuation">}</span><br> res<br><span class="hljs-punctuation">}</span><br>require<span class="hljs-punctuation">(</span>reshape2<span class="hljs-punctuation">)</span><br>f_matrix_heatmap <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-comment"># 标准化一下</span><br><span class="hljs-comment"># dfA <- as.data.frame(scale(dfA))</span><br> <span class="hljs-comment"># 转换前，先增加一列ID列，保存行名字</span><br> dfA<span class="hljs-operator">$</span>df_ID <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># dfA$df_ID <- factor(x = dfA$df_ID, ordered = T)</span><br> dfm <span class="hljs-operator"><-</span> melt<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">,</span> na.rm <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> id.vars <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'df_ID'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> dfm<span class="hljs-operator">$</span>variable <span class="hljs-operator"><-</span> factor<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>dfm<span class="hljs-operator">$</span>variable<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ordered <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> ggplot<span class="hljs-punctuation">(</span>dfm<span class="hljs-punctuation">,</span> aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>variable<span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span>df_ID<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> geom_tile<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>fill<span class="hljs-operator">=</span>value<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> scale_fill_gradient<span class="hljs-punctuation">(</span>low <span class="hljs-operator">=</span> <span class="hljs-string">"white"</span><span class="hljs-punctuation">,</span> high <span class="hljs-operator">=</span> <span class="hljs-string">"red"</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> xlab<span class="hljs-punctuation">(</span><span class="hljs-string">"samples"</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme_bw<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>panel.grid.major <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>legend.key<span class="hljs-operator">=</span>element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p <span class="hljs-operator"><-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>angle<span class="hljs-operator">=</span><span class="hljs-number">45</span><span class="hljs-punctuation">,</span> hjust<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> vjust<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> p<br><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></pre></td><td class="code"><pre><code class="hljs r">immune<span class="hljs-punctuation">[[</span><span class="hljs-string">'tmp2'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> paste<span class="hljs-punctuation">(</span><span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">[[</span><span class="hljs-string">'immune_type_2'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">[[</span><span class="hljs-string">'patient_id'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br>tmp2 <span class="hljs-operator"><-</span> f_matrix_groupMean<span class="hljs-punctuation">(</span>immune<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<span class="hljs-punctuation">[</span>unlist<span class="hljs-punctuation">(</span>sR<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> immune<span class="hljs-punctuation">[[</span><span class="hljs-string">'tmp2'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>p2 <span class="hljs-operator"><-</span> f_matrix_heatmap<span class="hljs-punctuation">(</span>tmp2<span class="hljs-punctuation">)</span><br>ggsave<span class="hljs-punctuation">(</span>p2<span class="hljs-punctuation">,</span> filename <span class="hljs-operator">=</span> <span class="hljs-string">'HSPC vs CRPC_heatmap_2.pdf'</span><span class="hljs-punctuation">,</span> dpi <span class="hljs-operator">=</span> <span class="hljs-number">1200</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">24</span><span class="hljs-punctuation">,</span> device <span class="hljs-operator">=</span> <span class="hljs-string">'pdf'</span><span class="hljs-punctuation">,</span> limitsize <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
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-
- <script>
- Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
- Fluid.plugins.fancyBox();
- });
- </script>
- <script>Fluid.plugins.imageCaption();</script>
- <script src="/js/local-search.js" ></script>
- <!-- 主题的启动项，将它保持在最底部 -->
- <!-- the boot of the theme, keep it at the bottom -->
- <script src="/js/boot.js" ></script>
-
- <noscript>
- <div class="noscript-warning">Blog works best with JavaScript enabled</div>
- </noscript>
- <!-- hexo injector body_end start -->
- <script defer src="/theme-inject/timeliness.js"></script>
- <!-- hexo injector body_end end --></body>
- </html>
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