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            <h1 id="seo-header">scMetabolism绘制代谢基因</h1>
            
            
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                <h2 id="定义绘图函数"><a href="#定义绘图函数" class="headerlink" title="定义绘图函数"></a>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></pre></td><td class="code"><pre><code class="hljs r"><span class="hljs-comment"># 绘制热图</span><br>f_metaG2G <span class="hljs-operator">&lt;-</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">&#123;</span><br>    res  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    alltype <span class="hljs-operator">&lt;-</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">&#123;</span><br>        res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</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">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;-&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;.&#x27;</span><span class="hljs-punctuation">,</span>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">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>f_matrix_groupMean <span class="hljs-operator">&lt;-</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">&#123;</span><br>    res <span class="hljs-operator">&lt;-</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">&lt;-</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">&#123;</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">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</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">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</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">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>reshape2<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>f_matrix_heatmap <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">,</span> levels <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-comment"># 转换前，先增加一列ID列，保存行名字</span><br>    dfA<span class="hljs-operator">$</span>df_ID <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">)</span><br>    dfm <span class="hljs-operator">&lt;-</span> melt<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">,</span> na.rm <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> id.vars <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;df_ID&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    dfm<span class="hljs-operator">$</span>variable <span class="hljs-operator">&lt;-</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">$</span>variable<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ordered <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>levels<span class="hljs-punctuation">)</span> <span class="hljs-operator">&gt;</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        dfm<span class="hljs-operator">$</span>df_ID  <span class="hljs-operator">&lt;-</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>df_ID<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> levels <span class="hljs-operator">=</span> rev<span class="hljs-punctuation">(</span>levels<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    p <span class="hljs-operator">&lt;-</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">&lt;-</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><span class="hljs-comment">#     p &lt;- p + scale_fill_gradient(low = &#x27;white&#x27;, high = &#x27;red&#x27;)</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> scale_fill_gradientn<span class="hljs-punctuation">(</span>colours <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;#3E5CC5&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;#65B48E&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;#E6EB00&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;#E64E00&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     p &lt;- p + scale_color_distiller(palette = &quot;Spectral&quot;)</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> xlab<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;samples&quot;</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">&lt;-</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">&lt;-</span> p <span class="hljs-operator">+</span> labs<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 删除xy轴标题 </span><br>    p<br><span class="hljs-punctuation">&#125;</span><br><br><span class="hljs-comment"># 提取代谢基因</span><br>require<span class="hljs-punctuation">(</span>stringr<span class="hljs-punctuation">)</span><br>f_KEGG_name2id <span class="hljs-operator">&lt;-</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">&#123;</span><br>    res <span class="hljs-operator">&lt;-</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">&#123;</span><br>        fuck <span class="hljs-operator">&lt;-</span> gsub<span class="hljs-punctuation">(</span>pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\\(&#x27;</span><span class="hljs-punctuation">,</span> replacement <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\\\\(&#x27;</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">&lt;-</span> gsub<span class="hljs-punctuation">(</span>pattern <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\\)&#x27;</span><span class="hljs-punctuation">,</span> replacement <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;\\\\)&#x27;</span><span class="hljs-punctuation">,</span> x <span class="hljs-operator">=</span> fuck<span class="hljs-punctuation">)</span><br>        idx <span class="hljs-operator">&lt;-</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">&lt;-</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">&#123;</span><br>            tmp <span class="hljs-operator">&lt;-</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">&lt;-</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">&lt;-</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">&#125;</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">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            print<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>KEGGREST<span class="hljs-punctuation">)</span><br>f_KEGG_id2symbol <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>KEGGid<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</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">&#123;</span><br>        hsa_info <span class="hljs-operator">&lt;-</span> keggGet<span class="hljs-punctuation">(</span>hsa_id<span class="hljs-punctuation">)</span><br>        hsa_info <span class="hljs-operator">&lt;-</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">&lt;-</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">&lt;-</span> strsplit<span class="hljs-punctuation">(</span>hsa_info<span class="hljs-punctuation">,</span>split <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;;&#x27;</span><span class="hljs-punctuation">)</span><br>        hsa_info <span class="hljs-operator">&lt;-</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">&#123;</span>X<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>        res <span class="hljs-operator">&lt;-</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">&#125;</span><br>    res <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</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">&#x27;\\] \\[&#x27;</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">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="获取绘图数据"><a href="#获取绘图数据" class="headerlink" title="获取绘图数据"></a>获取绘图数据</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></pre></td><td class="code"><pre><code class="hljs r">immune <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../figure1.cellTypeist/immune.rds&#x27;</span><span class="hljs-punctuation">)</span><br>immune<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;tmp&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</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">&#x27;immune_type_2&#x27;</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">&#x27;group&#x27;</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>M_c <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">,</span> cell_type <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;Myeloid&#x27;</span><span class="hljs-punctuation">)</span><br>L_c <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">,</span> cell_type <span class="hljs-operator">!=</span> <span class="hljs-string">&#x27;Myeloid&#x27;</span><span class="hljs-punctuation">)</span><br><br>M_m <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;selected_for_gene_M.CSV&#x27;</span><span class="hljs-punctuation">,</span> header <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>L_m <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;selected_for_gene_L.CSV&#x27;</span><span class="hljs-punctuation">,</span> header <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br><br>keggL <span class="hljs-operator">&lt;-</span> keggList<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;pathway&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;hsa&quot;</span><span class="hljs-punctuation">)</span><br><br>M_g <span class="hljs-operator">&lt;-</span> f_KEGG_name2id<span class="hljs-punctuation">(</span>keggL<span class="hljs-punctuation">,</span> unlist<span class="hljs-punctuation">(</span>M_m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>M_g <span class="hljs-operator">&lt;-</span> f_KEGG_id2symbol<span class="hljs-punctuation">(</span>M_g<span class="hljs-punctuation">)</span><br>M_g <span class="hljs-operator">&lt;-</span> M_g<span class="hljs-punctuation">[</span>M_g <span class="hljs-operator">%in%</span> rownames<span class="hljs-punctuation">(</span>M_c<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br><br>L_g <span class="hljs-operator">&lt;-</span> f_KEGG_name2id<span class="hljs-punctuation">(</span>keggL<span class="hljs-punctuation">,</span> unlist<span class="hljs-punctuation">(</span>L_m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>L_g <span class="hljs-operator">&lt;-</span> f_KEGG_id2symbol<span class="hljs-punctuation">(</span>L_g<span class="hljs-punctuation">)</span><br>L_g <span class="hljs-operator">&lt;-</span> L_g<span class="hljs-punctuation">[</span>L_g <span class="hljs-operator">%in%</span> rownames<span class="hljs-punctuation">(</span>L_c<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br></code></pre></td></tr></table></figure>

<h2 id="绘图并保存"><a href="#绘图并保存" class="headerlink" title="绘图并保存"></a>绘图并保存</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></pre></td><td class="code"><pre><code class="hljs r">M_p <span class="hljs-operator">&lt;-</span> f_matrix_heatmap<span class="hljs-punctuation">(</span>f_matrix_groupMean<span class="hljs-punctuation">(</span>M_c<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>RNA<span class="hljs-operator">@</span>data<span class="hljs-punctuation">[</span>M_g<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> M_c<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;tmp&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> matrixN <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> levels <span class="hljs-operator">=</span> M_g<span class="hljs-punctuation">)</span><br><br>ggsave<span class="hljs-punctuation">(</span>M_p<span class="hljs-punctuation">,</span> filename <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;scMetabolism_gene_M.pdf&#x27;</span><span class="hljs-punctuation">,</span> dpi <span class="hljs-operator">=</span> <span class="hljs-number">1200</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">32</span><span class="hljs-punctuation">,</span> device <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;pdf&#x27;</span><span class="hljs-punctuation">,</span> limitsize <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br><br>L_p <span class="hljs-operator">&lt;-</span> f_matrix_heatmap<span class="hljs-punctuation">(</span>f_matrix_groupMean<span class="hljs-punctuation">(</span>L_c<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>RNA<span class="hljs-operator">@</span>data<span class="hljs-punctuation">[</span>L_g<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> L_c<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;tmp&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><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> levels <span class="hljs-operator">=</span> L_g<span class="hljs-punctuation">)</span><br><br>ggsave<span class="hljs-punctuation">(</span>L_p<span class="hljs-punctuation">,</span> filename <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;scMetabolism_gene_L.pdf&#x27;</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">6</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">48</span><span class="hljs-punctuation">,</span> device <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;pdf&#x27;</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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