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- <h1 id="seo-header">scMetabolism比较绘图</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></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>require<span class="hljs-punctuation">(</span>ggplot2<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> levels <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-comment"># 转换前,先增加一列ID列,保存行名字</span><br> dfA<span class="hljs-operator">$</span>df_ID <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">)</span><br> dfm <span class="hljs-operator"><-</span> melt<span class="hljs-punctuation">(</span>dfA<span class="hljs-punctuation">,</span> na.rm <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> id.vars <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'df_ID'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> dfm<span class="hljs-operator">$</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">$</span>variable<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ordered <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>levels<span class="hljs-punctuation">)</span> <span class="hljs-operator">></span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> dfm<span class="hljs-operator">$</span>df_ID <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>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">}</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><span class="hljs-comment"># p <- p + scale_fill_gradient(low = 'white', high = 'red')</span><br> p <span class="hljs-operator"><-</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">'#3E5CC5'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'#65B48E'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'#E6EB00'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'#E64E00'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># p <- p + scale_color_distiller(palette = "Spectral")</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 <span class="hljs-operator"><-</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">}</span><br></code></pre></td></tr></table></figure>
- <h2 id="绘图"><a href="#绘图" class="headerlink" title="绘图"></a>绘图</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br></pre></td><td class="code"><pre><code class="hljs r"><span class="hljs-comment"># 01.组合metadata</span><br>immune<span class="hljs-punctuation">[[</span><span class="hljs-string">'tmp'</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">'group'</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><span class="hljs-comment"># 02.切分感兴趣的细胞群并计算代谢强度</span><br>M_c <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>immune<span class="hljs-punctuation">,</span> cell_type <span class="hljs-operator">==</span> <span class="hljs-string">'Myeloid'</span><span class="hljs-punctuation">)</span><br>M_c <span class="hljs-operator"><-</span> sc.metabolism.Seurat<span class="hljs-punctuation">(</span>obj <span class="hljs-operator">=</span> M_c<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><span class="hljs-comment">#03.读入感兴趣的通路</span><br>sM_h <span class="hljs-operator"><-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">'selected_pathway_high.CSV'</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>sM_m <span class="hljs-operator"><-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">'selected_pathway_medium.CSV'</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>sM_l <span class="hljs-operator"><-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">'selected_pathway_low.CSV'</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><span class="hljs-comment">#04.调用绘图函数</span><br>P7_h <span class="hljs-operator"><-</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>METABOLISM<span class="hljs-operator">$</span>score<span class="hljs-punctuation">[</span>unlist<span class="hljs-punctuation">(</span>sM_h<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> M_c<span class="hljs-punctuation">[[</span><span class="hljs-string">'tmp'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> levels <span class="hljs-operator">=</span> unlist<span class="hljs-punctuation">(</span>sM_h<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span>element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>P7_m <span class="hljs-operator"><-</span> f_matrix_heatmap<span class="hljs-punctuation">(</span>f_matrix_groupMean<span class="hljs-punctuation">(</span>M_c<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<span class="hljs-punctuation">[</span>unlist<span class="hljs-punctuation">(</span>sM_m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> M_c<span class="hljs-punctuation">[[</span><span class="hljs-string">'tmp'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> levels <span class="hljs-operator">=</span> unlist<span class="hljs-punctuation">(</span>sM_m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span>element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>P7_l <span class="hljs-operator"><-</span> f_matrix_heatmap<span class="hljs-punctuation">(</span>f_matrix_groupMean<span class="hljs-punctuation">(</span>M_c<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>METABOLISM<span class="hljs-operator">$</span>score<span class="hljs-punctuation">[</span>unlist<span class="hljs-punctuation">(</span>sM_l<span class="hljs-punctuation">)</span><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">'tmp'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> levels <span class="hljs-operator">=</span> unlist<span class="hljs-punctuation">(</span>sM_l<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#05.组合绘图</span><br>require<span class="hljs-punctuation">(</span>patchwork<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>dplyr<span class="hljs-punctuation">)</span><br>P7 <span class="hljs-operator"><-</span> <span class="hljs-punctuation">(</span>P7_h <span class="hljs-operator">/</span> P7_m <span class="hljs-operator">/</span> P7_l<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> plot_layout<span class="hljs-punctuation">(</span>nrow <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> heights <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>sM_h<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>sM_m<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nrow<span class="hljs-punctuation">(</span>sM_l<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#06。保存绘图结果</span><br>ggsave<span class="hljs-punctuation">(</span>P7<span class="hljs-punctuation">,</span> filename <span class="hljs-operator">=</span> <span class="hljs-string">'HSPC vs CRPC_M.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">12</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">10</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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