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            <h1 id="seo-header">Seurat绘制指定基因的小提琴图</h1>
            
            
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                <h2 id="第一步-定义绘图函数"><a href="#第一步-定义绘图函数" class="headerlink" title="第一步 定义绘图函数"></a>第一步 定义绘图函数</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br></pre></td><td class="code"><pre><code class="hljs r">f_VlnBoxPlot_gene <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">,</span> sampleN<span class="hljs-punctuation">,</span> geneN<span class="hljs-punctuation">,</span> rmZero<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> data.frame<span class="hljs-punctuation">(</span>geneID<span class="hljs-operator">=</span>colnames<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;groupN&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> scRNAo<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>res<span class="hljs-operator">$</span>geneID<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;sampleN&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> scRNAo<span class="hljs-punctuation">[[</span>sampleN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>res<span class="hljs-operator">$</span>geneID<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;value&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> scRNAo<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>RNA<span class="hljs-operator">@</span>data<span class="hljs-punctuation">[</span>geneN<span class="hljs-punctuation">,</span> res<span class="hljs-operator">$</span>geneID<span class="hljs-punctuation">]</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>rmZero<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        subset<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> value <span class="hljs-operator">&gt;</span> <span class="hljs-number">0</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<br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>f_VlnBoxPlot_df <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> geneN<span class="hljs-punctuation">,</span> groupN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;groupN&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    p <span class="hljs-operator">&lt;-</span> ggplot<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span><span class="hljs-operator">!</span><span class="hljs-operator">!</span>sym<span class="hljs-punctuation">(</span>groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span>value<span class="hljs-punctuation">,</span> fill<span class="hljs-operator">=</span> <span class="hljs-operator">!</span><span class="hljs-operator">!</span>sym<span class="hljs-punctuation">(</span>groupN<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_bw<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> NoLegend<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_violin<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 绘制小提琴图</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> stat_ydensity<span class="hljs-punctuation">(</span>trim <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> scale <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;width&#x27;</span><span class="hljs-punctuation">,</span> adjust <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 绘制小提琴图</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> geom_boxplot<span class="hljs-punctuation">(</span>width<span class="hljs-operator">=</span><span class="hljs-number">0.618</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 绘制箱型图</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> stat_summary<span class="hljs-punctuation">(</span>fun<span class="hljs-operator">=</span><span class="hljs-string">&quot;mean&quot;</span><span class="hljs-punctuation">,</span>geom<span class="hljs-operator">=</span><span class="hljs-string">&quot;point&quot;</span><span class="hljs-punctuation">,</span>color<span class="hljs-operator">=</span><span class="hljs-string">&#x27;white&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 添加均值点</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 <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> scale_y_continuous<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">,</span> breaks <span class="hljs-operator">=</span> <span class="hljs-built_in">floor</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">max</span><span class="hljs-punctuation">(</span>layer_scales<span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>y<span class="hljs-operator">$</span><span class="hljs-built_in">range</span><span class="hljs-operator">$</span><span class="hljs-built_in">range</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 美化y轴刻度</span><br><span class="hljs-comment">#     p &lt;- p + theme(panel.background = element_rect(colour=&quot;black&quot;)) # 添加框线</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>plot.margin <span class="hljs-operator">=</span> unit<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;cm&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 尽量删除图外空白</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> facet_grid<span class="hljs-punctuation">(</span>sampleN <span class="hljs-operator">~</span> .<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 添加分页</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> labs<span class="hljs-punctuation">(</span>title <span class="hljs-operator">=</span> geneN<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><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>hjust <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> angle <span class="hljs-operator">=</span> <span class="hljs-number">45</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    p<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
                
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