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            <h1 id="seo-header">Seurat绘制小提琴图与箱型图的叠加图</h1>
            
            
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                <h2 id="第一步-准备测试数据"><a href="#第一步-准备测试数据" class="headerlink" title="第一步 准备测试数据"></a>第一步 准备测试数据</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></pre></td><td class="code"><pre><code class="hljs r">library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>SeuratData<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>patchwork<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>dplyr<span class="hljs-punctuation">)</span><br>InstallData<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;pbmc3k&#x27;</span><span class="hljs-punctuation">)</span><br>pbmc3k<br>Idents<span class="hljs-punctuation">(</span>pbmc3k<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> pbmc3k<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;seurat_annotations&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br></code></pre></td></tr></table></figure>

<h2 id="第二步-尝试拼图"><a href="#第二步-尝试拼图" class="headerlink" title="第二步 尝试拼图"></a>第二步 尝试拼图</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</span><br><span class="line">88</span><br><span class="line">89</span><br><span class="line">90</span><br><span class="line">91</span><br><span class="line">92</span><br><span class="line">93</span><br><span class="line">94</span><br><span class="line">95</span><br><span class="line">96</span><br><span class="line">97</span><br></pre></td><td class="code"><pre><code class="hljs r">require<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggfun<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggplotify<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>aplot<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>cowplot<span class="hljs-punctuation">)</span><br>f_VlnBoxPlot_0 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> feature<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    vp <span class="hljs-operator">&lt;-</span> VlnPlot<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> feature<span class="hljs-punctuation">,</span> slot <span class="hljs-operator">=</span> <span class="hljs-string">&quot;counts&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">log</span> <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><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> <span class="hljs-comment"># 获取数据</span><br>    colnames<span class="hljs-punctuation">(</span>vp<span class="hljs-operator">$</span>data<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;GENE&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;ident&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 统一mapping的名称</span><br>    p <span class="hljs-operator">&lt;-</span> ggplot<span class="hljs-punctuation">(</span>vp<span class="hljs-operator">$</span>data<span class="hljs-punctuation">,</span> aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>ident<span class="hljs-punctuation">,</span>y<span class="hljs-operator">=</span>GENE<span class="hljs-punctuation">,</span>fill<span class="hljs-operator">=</span>ident<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> vp<span class="hljs-operator">$</span>theme <span class="hljs-comment"># 重构绘图</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-operator">+</span> scale_y_continuous<span class="hljs-punctuation">(</span>trans <span class="hljs-operator">=</span> <span class="hljs-string">&quot;log10&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 绘制小提琴图，对y轴进行log10缩放</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> theme<span class="hljs-punctuation">(</span>plot.title<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-comment"># 删除总标题</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>feature<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 删除x轴标题，y标题改成基因名</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.title.y<span class="hljs-operator">=</span>element_text<span class="hljs-punctuation">(</span>vjust<span class="hljs-operator">=</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span>angle<span class="hljs-operator">=</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># y标题垂直居中、水平显示</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_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 删除x轴刻度</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>panel.background <span class="hljs-operator">=</span> element_rect<span class="hljs-punctuation">(</span>colour<span class="hljs-operator">=</span><span class="hljs-string">&quot;black&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 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>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_VlnBoxPlot_1 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> feature_type<span class="hljs-punctuation">,</span> features<span class="hljs-punctuation">,</span> isLast<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    feature <span class="hljs-operator">=</span> features<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    p <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_0<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> feature<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>features<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>        <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>feature <span class="hljs-keyword">in</span> features<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>features<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">/</span> f_VlnBoxPlot_0<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> feature<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>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>isLast<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</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">0.5</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> <span class="hljs-comment"># 添加x轴坐标</span><br>    <span class="hljs-punctuation">&#125;</span><br>    p <span class="hljs-operator">&lt;-</span> as.ggplot<span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> facet_set<span class="hljs-punctuation">(</span>feature_type<span class="hljs-punctuation">,</span> side <span class="hljs-operator">=</span> <span class="hljs-string">&quot;r&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 添加基因集说明</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>strip.text.y <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>size <span class="hljs-operator">=</span> <span class="hljs-number">15</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 设置说明文字大小</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>f_VlnBoxPlot_2 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    markers <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>celltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    feature_types  <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>celltype<span class="hljs-punctuation">)</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>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>feature_type <span class="hljs-keyword">in</span> feature_types<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-punctuation">[[</span>feature_type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nrow<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        feature_type <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span>lc_i<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;celltype&#x27;</span><span class="hljs-punctuation">]</span><br>        feature <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span>lc_i<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;marker&#x27;</span><span class="hljs-punctuation">]</span><br>        res<span class="hljs-punctuation">[[</span>feature_type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">[[</span>feature_type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> feature<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>pushR <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>foo<span class="hljs-punctuation">,</span> bar<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>  foo<span class="hljs-punctuation">[[</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>foo<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> <span class="hljs-operator">&lt;-</span> bar<br>  foo<br><span class="hljs-punctuation">&#125;</span><br>popR <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>foo<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>  foo<span class="hljs-punctuation">[[</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>foo<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br>f_VlnBoxPlot <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> lc_markers<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    markers <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_2<span class="hljs-punctuation">(</span>lc_markers<span class="hljs-punctuation">)</span><br>    feature_types  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><br>    last_feature_type <span class="hljs-operator">&lt;-</span> feature_types<span class="hljs-punctuation">[</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>feature_types<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    feature_type <span class="hljs-operator">&lt;-</span> feature_types<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    p <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_1<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> feature_type<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">[[</span>feature_type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> feature_type<span class="hljs-operator">==</span>last_feature_type<span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     plist &lt;- list()</span><br><span class="hljs-comment">#     plist &lt;- pushR(plist, p)</span><br><span class="hljs-comment">#     p1 &lt;- p # 作为参考标准图</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>feature_types<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>        <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>feature_type <span class="hljs-keyword">in</span> feature_types<span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>feature_types<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            p2 <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_1<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> feature_type<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">[[</span>feature_type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> feature_type<span class="hljs-operator">==</span>last_feature_type<span class="hljs-punctuation">)</span><br><span class="hljs-comment">#             plist &lt;- pushR(plist, p2)</span><br><span class="hljs-comment">#             p2 &lt;- p2 + xlim2(p1) # x轴与p1对齐</span><br>            p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">/</span> p2<br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-comment">#     p &lt;- as.ggplot(p + theme(axis.text.x=element_text(hjust=0.5,angle=45))) # 添加x轴坐标</span><br><span class="hljs-comment">#     p &lt;- plot_grid(plotlist = plist, ncol = 1, align = &quot;v&quot;)</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>markers <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span>header <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> text <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;</span><br><span class="hljs-string">celltype,marker</span><br><span class="hljs-string">Naive CD4+ T,IL7R</span><br><span class="hljs-string">Naive CD4+ T,CCR7</span><br><span class="hljs-string">CD14+ Mono,CD14</span><br><span class="hljs-string">CD14+ Mono,LYZ</span><br><span class="hljs-string">Memory CD4+,S100A4</span><br><span class="hljs-string">B,MS4A1</span><br><span class="hljs-string">CD8+ T,CD8A</span><br><span class="hljs-string">FCGR3A+ Mono,FCGR3A</span><br><span class="hljs-string">FCGR3A+ Mono,MS4A7</span><br><span class="hljs-string">NK,GNLY</span><br><span class="hljs-string">NK,NKG7</span><br><span class="hljs-string">DC,FCER1A</span><br><span class="hljs-string">DC,CST3</span><br><span class="hljs-string">Platelet,PPBP</span><br><span class="hljs-string">&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">c</span> <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot<span class="hljs-punctuation">(</span>pbmc3k<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">)</span><br><span class="hljs-built_in">c</span><br></code></pre></td></tr></table></figure>

<h2 id="第三步-尝试分面"><a href="#第三步-尝试分面" class="headerlink" title="第三步 尝试分面"></a>第三步 尝试分面</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 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class="line">119</span><br><span class="line">120</span><br><span class="line">121</span><br><span class="line">122</span><br><span class="line">123</span><br><span class="line">124</span><br><span class="line">125</span><br><span class="line">126</span><br><span class="line">127</span><br><span class="line">128</span><br><span class="line">129</span><br><span class="line">130</span><br><span class="line">131</span><br><span class="line">132</span><br><span class="line">133</span><br><span class="line">134</span><br><span class="line">135</span><br><span class="line">136</span><br><span class="line">137</span><br><span class="line">138</span><br><span class="line">139</span><br><span class="line">140</span><br><span class="line">141</span><br><span class="line">142</span><br><span class="line">143</span><br><span class="line">144</span><br><span class="line">145</span><br><span class="line">146</span><br><span class="line">147</span><br><span class="line">148</span><br><span class="line">149</span><br><span class="line">150</span><br><span class="line">151</span><br><span class="line">152</span><br><span class="line">153</span><br><span class="line">154</span><br><span class="line">155</span><br><span class="line">156</span><br><span class="line">157</span><br><span class="line">158</span><br><span class="line">159</span><br><span class="line">160</span><br><span class="line">161</span><br><span class="line">162</span><br><span class="line">163</span><br><span class="line">164</span><br><span class="line">165</span><br><span class="line">166</span><br><span class="line">167</span><br><span class="line">168</span><br><span class="line">169</span><br><span class="line">170</span><br><span class="line">171</span><br><span class="line">172</span><br><span class="line">173</span><br><span class="line">174</span><br><span class="line">175</span><br><span class="line">176</span><br><span class="line">177</span><br><span class="line">178</span><br><span class="line">179</span><br><span class="line">180</span><br><span class="line">181</span><br><span class="line">182</span><br><span class="line">183</span><br><span class="line">184</span><br><span class="line">185</span><br><span class="line">186</span><br><span class="line">187</span><br><span class="line">188</span><br><span class="line">189</span><br><span class="line">190</span><br><span class="line">191</span><br><span class="line">192</span><br><span class="line">193</span><br><span class="line">194</span><br><span class="line">195</span><br><span class="line">196</span><br><span class="line">197</span><br><span class="line">198</span><br><span class="line">199</span><br><span class="line">200</span><br><span class="line">201</span><br><span class="line">202</span><br><span class="line">203</span><br><span class="line">204</span><br><span class="line">205</span><br><span class="line">206</span><br><span class="line">207</span><br><span class="line">208</span><br><span class="line">209</span><br><span class="line">210</span><br><span class="line">211</span><br><span class="line">212</span><br><span class="line">213</span><br><span class="line">214</span><br><span class="line">215</span><br><span class="line">216</span><br></pre></td><td class="code"><pre><code class="hljs r">f_VlnBoxPlot_18 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>features<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tb <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>features<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    tb <span class="hljs-operator">&lt;-</span> tb<span class="hljs-punctuation">[</span>tb<span class="hljs-operator">$</span>Freq <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>tb<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_VlnBoxPlot_19 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> features<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    dupl <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_18<span class="hljs-punctuation">(</span>features<span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>dupl<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nrow<span class="hljs-punctuation">(</span>dupl<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        dupfeature <span class="hljs-operator">&lt;-</span> dupl<span class="hljs-punctuation">[</span>lc_i<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;features&#x27;</span><span class="hljs-punctuation">]</span><br>        idx <span class="hljs-operator">&lt;-</span> which<span class="hljs-punctuation">(</span>features <span class="hljs-operator">==</span> dupfeature<span class="hljs-punctuation">)</span><br>        <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>lc_j <span class="hljs-keyword">in</span> <span class="hljs-number">2</span><span class="hljs-operator">:</span>dupl<span class="hljs-punctuation">[</span>lc_i<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Freq&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            newfeature <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span>dupfeature<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;.&#x27;</span><span class="hljs-punctuation">,</span>lc_j<span class="hljs-punctuation">)</span><br><span class="hljs-comment">#             features[[idx[lc_j]]] &lt;- newfeature</span><br><span class="hljs-comment">#             tmp[[newfeature]] &lt;- tmp[[dupfeature]]</span><br>            colnames<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[[</span>idx<span class="hljs-punctuation">[</span>lc_j<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> newfeature<br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-comment">#     tmp &lt;- tmp[,c(features, groupN)]</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_VlnBoxPlot_20 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> features<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tmp <span class="hljs-operator">&lt;-</span> log1p<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;RNA&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">@</span>counts<span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     tmp &lt;- scRNAo[[&#x27;RNA&#x27;]]@counts</span><br>    tmp <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>as.matrix<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[</span>features<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>    types <span class="hljs-operator">&lt;-</span> scRNAo<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    types<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span>types<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 确保是因子</span><br>    newLevels <span class="hljs-operator">&lt;-</span> levels<span class="hljs-punctuation">(</span>types<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    newLevels <span class="hljs-operator">&lt;-</span> newLevels<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>newLevels<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    types<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span>types<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> levels<span class="hljs-operator">=</span>newLevels<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 排序</span><br>    tmp <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> types<span class="hljs-punctuation">)</span><br>    tmp <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_19<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> features<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_setRowName <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_df<span class="hljs-punctuation">,</span> lc_colName<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_df <span class="hljs-operator">&lt;-</span> lc_df<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>lc_df<span class="hljs-punctuation">[[</span>lc_colName<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>    tp_index <span class="hljs-operator">&lt;-</span> duplicated<span class="hljs-punctuation">(</span>lc_df<span class="hljs-punctuation">[[</span>lc_colName<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    lc_df <span class="hljs-operator">&lt;-</span> lc_df<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span>tp_index<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>lc_df<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> lc_df<span class="hljs-punctuation">[[</span>lc_colName<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    lc_df<br><span class="hljs-punctuation">&#125;</span><br> <br>f_VlnBoxPlot_25 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    dupl <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_18<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>marker<span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>dupl<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>        <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>lc_i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span>nrow<span class="hljs-punctuation">(</span>dupl<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            dupfeature <span class="hljs-operator">&lt;-</span> dupl<span class="hljs-punctuation">[</span>lc_i<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;features&#x27;</span><span class="hljs-punctuation">]</span><br>            idx <span class="hljs-operator">&lt;-</span> which<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>marker <span class="hljs-operator">==</span> dupfeature<span class="hljs-punctuation">)</span><br>            <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>lc_j <span class="hljs-keyword">in</span> <span class="hljs-number">2</span><span class="hljs-operator">:</span>dupl<span class="hljs-punctuation">[</span>lc_i<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Freq&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>                newfeature <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span>dupfeature<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;.&#x27;</span><span class="hljs-punctuation">,</span>lc_j<span class="hljs-punctuation">)</span><br>                markers<span class="hljs-punctuation">[</span>idx<span class="hljs-punctuation">[</span>lc_j<span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;marker&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> newfeature<br>            <span class="hljs-punctuation">&#125;</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    markers <span class="hljs-operator">&lt;-</span> f_setRowName<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;marker&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 准备marker到类型的映射</span><br>    markers<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;celltype&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;celltype&#x27;</span><span class="hljs-punctuation">]</span><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>    col <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_col<span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>levels<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;celltype&#x27;</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>    markers<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;colour&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> col<span class="hljs-punctuation">[</span><span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;celltype&#x27;</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-built_in">return</span><span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>require<span class="hljs-punctuation">(</span>reshape2<span class="hljs-punctuation">)</span><br>f_VlnBoxPlot_21 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    data <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_20<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;marker&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 获取宽数据</span><br>    data <span class="hljs-operator">&lt;-</span> melt<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">,</span> id.vars <span class="hljs-operator">=</span> groupN<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 宽数据变长数据</span><br>    <br>    markers <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_25<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 准备marker到颜色的映射</span><br>    data<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;facet_fill_color&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span><span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;variable&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;colour&#x27;</span><span class="hljs-punctuation">]</span> <span class="hljs-comment"># 进行映射</span><br>    newLevels <span class="hljs-operator">&lt;-</span> data<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;facet_fill_color&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span><span class="hljs-operator">!</span>duplicated<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;facet_fill_color&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-comment"># 确保顺序</span><br>    data<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;facet_fill_color&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;facet_fill_color&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> levels<span class="hljs-operator">=</span>newLevels<span class="hljs-punctuation">)</span><br>    <br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_VlnBoxPlot_23 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    markers <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>celltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span> <span class="hljs-comment"># 确保顺序正确</span><br>    theme_s <span class="hljs-operator">&lt;-</span> VlnPlot<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> markers<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;marker&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> slot <span class="hljs-operator">=</span> <span class="hljs-string">&quot;counts&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">log</span> <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> group.by <span class="hljs-operator">=</span> groupN<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 借用 Seurat 的主题</span><br>    data <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_21<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 准备好数据</span><br>    p <span class="hljs-operator">&lt;-</span> ggplot<span class="hljs-punctuation">(</span>data<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_s<span class="hljs-operator">$</span>theme <span class="hljs-operator">+</span> NoLegend<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>  <span class="hljs-comment"># 借用 Seurat 的主题</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> theme<span class="hljs-punctuation">(</span>plot.title<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-comment"># 删除总标题</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>variable <span class="hljs-operator">~</span> .<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 添加分页</span><br>    nx <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">[[</span>groupN<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>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> scale_fill_manual<span class="hljs-punctuation">(</span>values<span class="hljs-operator">=</span>f_VlnBoxPlot_col<span class="hljs-punctuation">(</span>nx<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    x_r <span class="hljs-operator">&lt;-</span> layer_scales<span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><span class="hljs-operator">$</span>x<span class="hljs-operator">$</span><span class="hljs-built_in">range</span><span class="hljs-operator">$</span><span class="hljs-built_in">range</span> <span class="hljs-comment"># 保存x轴刻度</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span>element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 删除x轴刻度</span><br>    p <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_26<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">,</span> p<span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     layer_scales(p)$x$range$range &lt;- x_r </span><br>    nr <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>x_r<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-number">2</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> scale_x_continuous<span class="hljs-punctuation">(</span> <span class="hljs-comment"># 恢复x轴刻度</span><br>        limits <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">/</span>nr<span class="hljs-operator">/</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-operator">/</span>nr<span class="hljs-operator">/</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>        breaks <span class="hljs-operator">=</span> seq<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>length.out<span class="hljs-operator">=</span>nr<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">2</span><span class="hljs-operator">:</span><span class="hljs-punctuation">(</span>nr<span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br>        label <span class="hljs-operator">=</span> x_r<br>    <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">0.5</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>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>require<span class="hljs-punctuation">(</span>treeio<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>ggtree<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>tidytree<span class="hljs-punctuation">)</span><br><span class="hljs-comment"># require(aplot)</span><br>f_VlnBoxPlot_24 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    markers <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>celltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br><span class="hljs-comment">#     pstandard &lt;- ggplot(markers, aes(y = marker)) # 创建标准y轴顺序</span><br>    feature_types  <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>celltype<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 创建根节点</span><br>    feature_types <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>feature_types<span class="hljs-punctuation">)</span><br>    feature_types<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;root&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-string">&#x27; &#x27;</span><br>    feature_types <span class="hljs-operator">&lt;-</span> feature_types<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-string">&#x27;root&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;feature_types&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    colnames<span class="hljs-punctuation">(</span>feature_types<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> colnames<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><br>    <br>    y <span class="hljs-operator">=</span> as.phylo<span class="hljs-punctuation">(</span>rbind<span class="hljs-punctuation">(</span>feature_types<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 转换成树</span><br>    <br>    yy <span class="hljs-operator">=</span> as_tibble<span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span>  <span class="hljs-comment"># 统一叶子节点的颜色</span><br>    mutate<span class="hljs-punctuation">(</span>cat <span class="hljs-operator">=</span> ifelse<span class="hljs-punctuation">(</span>node <span class="hljs-operator">%in%</span> parent<span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> parent<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    yy<span class="hljs-operator">$</span>cat<span class="hljs-punctuation">[</span>rootnode<span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br>    <br>    p <span class="hljs-operator">&lt;-</span> ggtree<span class="hljs-punctuation">(</span>as.treedata<span class="hljs-punctuation">(</span>yy<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ladderize<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> layout<span class="hljs-operator">=</span><span class="hljs-string">&#x27;roundrect&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span>  <span class="hljs-comment"># 通过 ggtree 绘图</span><br>    geom_nodelab<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>x<span class="hljs-operator">*</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span> label<span class="hljs-operator">=</span>label<span class="hljs-punctuation">,</span> <br>                   fill<span class="hljs-operator">=</span>factor<span class="hljs-punctuation">(</span>cat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> hjust<span class="hljs-operator">=</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span> geom<span class="hljs-operator">=</span><span class="hljs-string">&#x27;text&#x27;</span><span class="hljs-punctuation">,</span> angle<span class="hljs-operator">=</span><span class="hljs-number">90</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <br>    geom_tiplab<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>label<span class="hljs-operator">=</span>label<span class="hljs-punctuation">,</span> fill<span class="hljs-operator">=</span>factor<span class="hljs-punctuation">(</span>cat<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> geom<span class="hljs-operator">=</span><span class="hljs-string">&#x27;text&#x27;</span><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">0.5</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    scale_y_reverse<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    hexpand<span class="hljs-punctuation">(</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> hexpand<span class="hljs-punctuation">(</span><span class="hljs-number">.06</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-operator">+</span> <br>    theme<span class="hljs-punctuation">(</span>legend.position <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;none&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     p &lt;- p + ylim2(pstandard) + scale_y_reverse() </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>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>require<span class="hljs-punctuation">(</span>ggplotify<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>gtable<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>grid<span class="hljs-punctuation">)</span><br>gtable_select <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span> <span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#123;</span><br>    matches <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">)</span><br>    x<span class="hljs-operator">$</span>layout <span class="hljs-operator">&lt;-</span> x<span class="hljs-operator">$</span>layout<span class="hljs-punctuation">[</span>matches<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">,</span> drop <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">]</span><br>    x<span class="hljs-operator">$</span>grobs <span class="hljs-operator">&lt;-</span> x<span class="hljs-operator">$</span>grobs<span class="hljs-punctuation">[</span>matches<span class="hljs-punctuation">]</span><br>    x<br><span class="hljs-punctuation">&#125;</span><br>gtable_stack <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>g1<span class="hljs-punctuation">,</span> g2<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    g1<span class="hljs-operator">$</span>grobs <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>g1<span class="hljs-operator">$</span>grobs<span class="hljs-punctuation">,</span> g2<span class="hljs-operator">$</span>grobs<span class="hljs-punctuation">)</span><br>    g1<span class="hljs-operator">$</span>layout <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>g1<span class="hljs-operator">$</span>layout<span class="hljs-punctuation">,</span> g2<span class="hljs-operator">$</span>layout<span class="hljs-punctuation">)</span><br>    g1<br><span class="hljs-punctuation">&#125;</span><br>f_VlnBoxPlot_26 <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dat<span class="hljs-punctuation">,</span> p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>strip.background<span class="hljs-operator">=</span>element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>  <span class="hljs-comment"># 去掉背景</span><br>    dummy <span class="hljs-operator">&lt;-</span> p <span class="hljs-comment"># 魔改出facet的填充</span><br>    dummy<span class="hljs-operator">$</span>layers <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    dummy <span class="hljs-operator">&lt;-</span> dummy <span class="hljs-operator">+</span> geom_rect<span class="hljs-punctuation">(</span>data<span class="hljs-operator">=</span>dat<span class="hljs-punctuation">,</span> xmin<span class="hljs-operator">=</span><span class="hljs-operator">-</span><span class="hljs-literal">Inf</span><span class="hljs-punctuation">,</span> ymin<span class="hljs-operator">=</span><span class="hljs-operator">-</span><span class="hljs-literal">Inf</span><span class="hljs-punctuation">,</span> xmax<span class="hljs-operator">=</span><span class="hljs-literal">Inf</span><span class="hljs-punctuation">,</span> ymax<span class="hljs-operator">=</span><span class="hljs-literal">Inf</span><span class="hljs-punctuation">,</span><br>                           aes<span class="hljs-punctuation">(</span>fill <span class="hljs-operator">=</span> facet_fill_color<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     print(dummy)</span><br>    g1 <span class="hljs-operator">&lt;-</span> ggplotGrob<span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br>    g2 <span class="hljs-operator">&lt;-</span> ggplotGrob<span class="hljs-punctuation">(</span>dummy<span class="hljs-punctuation">)</span><br>    panels <span class="hljs-operator">&lt;-</span> grepl<span class="hljs-punctuation">(</span>pattern<span class="hljs-operator">=</span><span class="hljs-string">&quot;panel&quot;</span><span class="hljs-punctuation">,</span> g2<span class="hljs-operator">$</span>layout<span class="hljs-operator">$</span>name<span class="hljs-punctuation">)</span><br>    strips <span class="hljs-operator">&lt;-</span> grepl<span class="hljs-punctuation">(</span>pattern<span class="hljs-operator">=</span><span class="hljs-string">&quot;strip-right&quot;</span><span class="hljs-punctuation">,</span> g2<span class="hljs-operator">$</span>layout<span class="hljs-operator">$</span>name<span class="hljs-punctuation">)</span><br>    g2<span class="hljs-operator">$</span>grobs<span class="hljs-punctuation">[</span>strips<span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> replicate<span class="hljs-punctuation">(</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>strips<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nullGrob<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> simplify <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>    g2<span class="hljs-operator">$</span>layout<span class="hljs-operator">$</span>l<span class="hljs-punctuation">[</span>panels<span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> g2<span class="hljs-operator">$</span>layout<span class="hljs-operator">$</span>l<span class="hljs-punctuation">[</span>panels<span class="hljs-punctuation">]</span> <span class="hljs-operator">+</span> <span class="hljs-number">1</span><br>    g2<span class="hljs-operator">$</span>layout<span class="hljs-operator">$</span>r<span class="hljs-punctuation">[</span>panels<span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> g2<span class="hljs-operator">$</span>layout<span class="hljs-operator">$</span>r<span class="hljs-punctuation">[</span>panels<span class="hljs-punctuation">]</span> <span class="hljs-operator">+</span> <span class="hljs-number">2</span><br>    new_strips <span class="hljs-operator">&lt;-</span> gtable_select<span class="hljs-punctuation">(</span>g2<span class="hljs-punctuation">,</span> panels  strips<span class="hljs-punctuation">)</span><br><span class="hljs-comment">#     print(as.ggplot(new_strips))</span><br>    new_plot <span class="hljs-operator">&lt;-</span> gtable_stack<span class="hljs-punctuation">(</span>g1<span class="hljs-punctuation">,</span> new_strips<span class="hljs-punctuation">)</span><br>    p <span class="hljs-operator">&lt;-</span> as.ggplot<span class="hljs-punctuation">(</span>new_plot<span class="hljs-punctuation">)</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>require<span class="hljs-punctuation">(</span>RColorBrewer<span class="hljs-punctuation">)</span><br>col_Paired <span class="hljs-operator">&lt;-</span> colorRampPalette<span class="hljs-punctuation">(</span>brewer.pal<span class="hljs-punctuation">(</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Paired&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>f_VlnBoxPlot_col <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>nx<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>nx <span class="hljs-operator">&lt;=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>brewer.pal<span class="hljs-punctuation">(</span>nx<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Paired&quot;</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>        <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>col_Paired<span class="hljs-punctuation">(</span>nx<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> <br>f_VlnBoxPlot <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    p2 <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_24<span class="hljs-punctuation">(</span>markers<span class="hljs-punctuation">)</span><br>    p <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_23<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers <span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><br>    p2 <span class="hljs-operator">+</span> p <span class="hljs-operator">+</span> plot_layout<span class="hljs-punctuation">(</span>ncol <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">,</span> widths <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>  <br><span class="hljs-punctuation">&#125;</span><br><br>f_VlnBoxPlot_simple <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    markers <span class="hljs-operator">&lt;-</span> markers<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>markers<span class="hljs-operator">$</span>celltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span> <span class="hljs-comment"># 确保顺序正确</span><br>    theme_s <span class="hljs-operator">&lt;-</span> VlnPlot<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> markers<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;marker&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> slot <span class="hljs-operator">=</span> <span class="hljs-string">&quot;counts&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">log</span> <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> group.by <span class="hljs-operator">=</span> groupN<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 借用 Seurat 的主题</span><br>    data <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_21<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> markers<span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 准备好数据</span><br>    p <span class="hljs-operator">&lt;-</span> ggplot<span class="hljs-punctuation">(</span>data<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_s<span class="hljs-operator">$</span>theme <span class="hljs-operator">+</span> NoLegend<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span>  <span class="hljs-comment"># 借用 Seurat 的主题</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> theme<span class="hljs-punctuation">(</span>plot.title<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-comment"># 删除总标题</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>variable <span class="hljs-operator">~</span> .<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 添加分页</span><br>    nx <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>unlist<span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">[[</span>groupN<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>    p <span class="hljs-operator">&lt;-</span> p <span class="hljs-operator">+</span> scale_fill_manual<span class="hljs-punctuation">(</span>values<span class="hljs-operator">=</span>f_VlnBoxPlot_col<span class="hljs-punctuation">(</span>nx<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    p <span class="hljs-operator">&lt;-</span> f_VlnBoxPlot_26<span class="hljs-punctuation">(</span>data<span class="hljs-punctuation">,</span> p<span class="hljs-punctuation">)</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="第四步-最终效果展示"><a href="#第四步-最终效果展示" class="headerlink" title="第四步 最终效果展示"></a>第四步 最终效果展示</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></pre></td><td class="code"><pre><code class="hljs r">markers <span class="hljs-operator">&lt;-</span> read.csv<span class="hljs-punctuation">(</span>header <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> text <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;</span><br><span class="hljs-string">celltype,marker</span><br><span class="hljs-string">Naive CD4+ T,IL7R</span><br><span class="hljs-string">Naive CD4+ T,CCR7</span><br><span class="hljs-string">CD14+ Mono,CD14</span><br><span class="hljs-string">CD14+ Mono,LYZ</span><br><span class="hljs-string">Memory CD4+,IL7R</span><br><span class="hljs-string">Memory CD4+,S100A4</span><br><span class="hljs-string">B,MS4A1</span><br><span class="hljs-string">CD8+ T,CD8A</span><br><span class="hljs-string">FCGR3A+ Mono,FCGR3A</span><br><span class="hljs-string">FCGR3A+ Mono,MS4A7</span><br><span class="hljs-string">NK,GNLY</span><br><span class="hljs-string">NK,NKG7</span><br><span class="hljs-string">DC,FCER1A</span><br><span class="hljs-string">DC,CST3</span><br><span class="hljs-string">Platelet,PPBP</span><br><span class="hljs-string">&#x27;</span><span class="hljs-punctuation">)</span><br><br>f_VlnBoxPlot<span class="hljs-punctuation">(</span>pbmc3k<span class="hljs-punctuation">,</span> markers <span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;seurat_annotations&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

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