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            <h1 id="seo-header">Seurat (九) hclust聚类分析 (二) by 细胞比例</h1>
            
            
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                <h2 id="第一步-读入数据"><a href="#第一步-读入数据" class="headerlink" title="第一步 读入数据"></a>第一步 读入数据</h2><p><a target="_blank" rel="noopener" href="https://limour.top/1334.html">Seurat (十) 同群细胞在不同脑区的DEGs （二）第二步</a></p>
<h2 id="第二步-构造相关计算函数"><a href="#第二步-构造相关计算函数" class="headerlink" title="第二步 构造相关计算函数"></a>第二步 构造相关计算函数</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br></pre></td><td class="code"><pre><code class="hljs r">f_ggplot2_ti <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>p<span class="hljs-punctuation">,</span> title<span class="hljs-punctuation">,</span> subtitle<span class="hljs-operator">=</span><span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>subtitle <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-punctuation">(</span>p <span class="hljs-operator">+</span> ggtitle<span class="hljs-punctuation">(</span>title<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-punctuation">(</span>p <span class="hljs-operator">+</span> ggtitle<span class="hljs-punctuation">(</span>title<span class="hljs-punctuation">,</span> subtitle<span class="hljs-operator">=</span>subtitle<span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <br>         theme<span class="hljs-punctuation">(</span>plot.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> plot.subtitle <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>hjust <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br> <br>library<span class="hljs-punctuation">(</span>ggdendro<span class="hljs-punctuation">)</span><br>f_ggdendrogram <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>hc<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    ggdendrogram<span class="hljs-punctuation">(</span>hc<span class="hljs-operator">$</span>h<span class="hljs-punctuation">,</span> rotate <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> size <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-operator">+</span>theme<span class="hljs-punctuation">(</span>axis.text <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">14</span><span class="hljs-punctuation">,</span>face <span class="hljs-operator">=</span> <span class="hljs-string">&quot;bold&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_hc <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    d <span class="hljs-operator">&lt;-</span> dist<span class="hljs-punctuation">(</span>t<span class="hljs-punctuation">(</span>lc_counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    h <span class="hljs-operator">&lt;-</span> hclust<span class="hljs-punctuation">(</span>d<span class="hljs-punctuation">)</span><br>    <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>d<span class="hljs-operator">=</span>d<span class="hljs-punctuation">,</span> h<span class="hljs-operator">=</span>h<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_hc_cop <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>hc<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    cop <span class="hljs-operator">&lt;-</span> cophenetic<span class="hljs-punctuation">(</span>hc<span class="hljs-operator">$</span>h<span class="hljs-punctuation">)</span><br>    cor<span class="hljs-punctuation">(</span>cop<span class="hljs-punctuation">,</span> hc<span class="hljs-operator">$</span>d<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br> <br>f_cluster_averages <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_scRNA<span class="hljs-punctuation">,</span> lc_metaN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ident&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-comment"># 切分出Clusters</span><br>    lc_clusters <span class="hljs-operator">&lt;-</span> SplitObject<span class="hljs-punctuation">(</span>lc_scRNA<span class="hljs-punctuation">,</span> split.by <span class="hljs-operator">=</span> lc_metaN<span class="hljs-punctuation">)</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><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>lc_clusters<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        lc_clusters<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> lc_clusters<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span>lc_clusters<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">@</span>active.assay<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">@</span>scale.data<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><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>lc_clusters<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        lc_clusters<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span>  <span class="hljs-operator">&lt;-</span> apply<span class="hljs-punctuation">(</span>lc_clusters<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>mean<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    lc_clusters <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>lc_clusters<span class="hljs-punctuation">)</span><br>    scale<span class="hljs-punctuation">(</span>lc_clusters<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br><br>f_br_cluster_f <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_filter <span class="hljs-operator">&lt;-</span> unlist<span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">[[</span>lc_groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    lc_filter <span class="hljs-operator">&lt;-</span> lc_filter<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>lc_filter<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    lc_filter<br><span class="hljs-punctuation">&#125;</span><br><br>f_br_cluster <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">,</span> lc_labelN<span class="hljs-punctuation">,</span> lc_prop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_all <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">[[</span>lc_labelN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    rownames<span class="hljs-punctuation">(</span>lc_all<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> lc_all<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    colnames<span class="hljs-punctuation">(</span>lc_all<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&quot;CB&quot;</span><br><span class="hljs-comment">#     lc_tp  &lt;- SplitObject(subset(x = sObject, !!sym(lc_groupN)%in%f_br_cluster_f(sObject, lc_groupN)), split.by = lc_groupN)</span><br>    lc_tp  <span class="hljs-operator">&lt;-</span> SplitObject<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> split.by <span class="hljs-operator">=</span> lc_groupN<span class="hljs-punctuation">)</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><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>lc_tp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>lc_prop<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            lc_tp<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> prop.table<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>lc_tp<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span>lc_labelN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>            lc_tp<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> table<span class="hljs-punctuation">(</span>lc_tp<span class="hljs-punctuation">[[</span>lc_i<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span>lc_labelN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>lc_name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_tp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        lc_all<span class="hljs-punctuation">[[</span>lc_name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br>        lc_all<span class="hljs-punctuation">[</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_tp<span class="hljs-punctuation">[[</span>lc_name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> lc_name<span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> lc_tp<span class="hljs-punctuation">[[</span>lc_name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><br>    lc_all<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<ul>
<li>相关性验证的代码</li>
</ul>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><code class="hljs r">library<span class="hljs-punctuation">(</span>Hmisc<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggcorrplot<span class="hljs-punctuation">)</span><br>f_corrplot <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_scdata<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_cor <span class="hljs-operator">&lt;-</span> rcorr<span class="hljs-punctuation">(</span>lc_scdata<span class="hljs-punctuation">)</span><br>    lc_cor<span class="hljs-operator">$</span>P<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>lc_cor<span class="hljs-operator">$</span>P<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-operator">=</span><span class="hljs-number">0</span><br>    ggcorrplot<span class="hljs-punctuation">(</span>lc_cor<span class="hljs-operator">$</span>r<span class="hljs-punctuation">,</span> type<span class="hljs-operator">=</span><span class="hljs-string">&quot;full&quot;</span><span class="hljs-punctuation">,</span>hc.order <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> lab <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> p.mat <span class="hljs-operator">=</span> lc_cor<span class="hljs-operator">$</span>P<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="第三步-（可选）筛选感兴趣的细胞群"><a href="#第三步-（可选）筛选感兴趣的细胞群" class="headerlink" title="第三步 （可选）筛选感兴趣的细胞群"></a>第三步 （可选）筛选感兴趣的细胞群</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></pre></td><td class="code"><pre><code class="hljs r">n_ExN <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;L4 IT&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L5 IT&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L5 ET&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;IT&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L6b&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L5/6 IT Car3&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L6 IT&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L2/3 IT&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L5/6 NP&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L6 IT Car3&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;L6 CT&#x27;</span><span class="hljs-punctuation">)</span><br> <br>n_InN <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Lamp5&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Pvalb&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Sst&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Vip&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Sncg&#x27;</span><span class="hljs-punctuation">)</span><br> <br>n_NoN <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Astro&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;PAX6&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Endo&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Micro-PVM&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;OPC&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Oligo&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Pericyte&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;VLMC&#x27;</span><span class="hljs-punctuation">)</span><br> <br>n_groups <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>NoN<span class="hljs-operator">=</span>n_NoN<span class="hljs-punctuation">,</span> ExN<span class="hljs-operator">=</span>n_ExN<span class="hljs-punctuation">,</span> InN<span class="hljs-operator">=</span>n_InN<span class="hljs-punctuation">)</span><br> <br>f_listUpdateRe <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_obj<span class="hljs-punctuation">,</span> lc_bool<span class="hljs-punctuation">,</span> lc_item<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_obj<span class="hljs-punctuation">[</span>lc_bool<span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>lc_item<span class="hljs-punctuation">,</span>times<span class="hljs-operator">=</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>lc_bool<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    lc_obj<br><span class="hljs-punctuation">&#125;</span><br> <br>f_grouplabel <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">,</span> lc_groups<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">&lt;-</span> lc_meta.data<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>lc_g <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_groups<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        lc_bool <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>res <span class="hljs-operator">%in%</span> lc_groups<span class="hljs-punctuation">[[</span>lc_g<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>c_n <span class="hljs-keyword">in</span> colnames<span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            lc_bool <span class="hljs-operator">=</span> lc_bool  <span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">[[</span>c_n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">%in%</span> lc_groups<span class="hljs-punctuation">[[</span>lc_g<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><br>        res <span class="hljs-operator">&lt;-</span> f_listUpdateRe<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> lc_bool<span class="hljs-punctuation">,</span> lc_g<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br><br>scRNA_split<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;n_groups&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> f_grouplabel<span class="hljs-punctuation">(</span>scRNA_split<span class="hljs-punctuation">[[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;hM1_hmca_class&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> n_groups<span class="hljs-punctuation">)</span><br><br>sc_Neuron  <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> scRNA_split<span class="hljs-punctuation">,</span> n_groups <span class="hljs-operator">%in%</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;InN&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;ExN&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="第四步-进行计算"><a href="#第四步-进行计算" class="headerlink" title="第四步 进行计算"></a>第四步 进行计算</h2><ul>
<li>by gene</li>
</ul>
<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></pre></td><td class="code"><pre><code class="hljs r">test_N <span class="hljs-operator">&lt;-</span> SplitObject<span class="hljs-punctuation">(</span>sc_Neuron<span class="hljs-punctuation">,</span> split.by <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;orig.ident&#x27;</span><span class="hljs-punctuation">)</span><br>test_N<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;all&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> sc_Neuron<br><br>listPN <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>n <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>test_N<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    test <span class="hljs-operator">=</span> f_cluster_averages<span class="hljs-punctuation">(</span>test_N<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Region&quot;</span><span class="hljs-punctuation">)</span><br>    hc <span class="hljs-operator">&lt;-</span> f_hc<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span><br>    cop <span class="hljs-operator">&lt;-</span> paste<span class="hljs-punctuation">(</span>n<span class="hljs-punctuation">,</span> hc <span class="hljs-operator">%&gt;%</span> f_hc_cop<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>cop<span class="hljs-punctuation">)</span><br>    listPN<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>f_hc<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_ggdendrogram<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_ggplot2_ti<span class="hljs-punctuation">(</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;hclust by gene in &#x27;</span><span class="hljs-punctuation">,</span> n<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> subtitle <span class="hljs-operator">=</span> cop<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    <span class="hljs-punctuation">(</span>f_corrplot<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_ggplot2_ti<span class="hljs-punctuation">(</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;cor by gene in &#x27;</span><span class="hljs-punctuation">,</span> n<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<ul>
<li>by proportion of cells</li>
</ul>
<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></pre></td><td class="code"><pre><code class="hljs r">test_s <span class="hljs-operator">&lt;-</span> SplitObject<span class="hljs-punctuation">(</span>scRNA_split<span class="hljs-punctuation">,</span> split.by <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;orig.ident&#x27;</span><span class="hljs-punctuation">)</span><br>test_s<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;all&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> scRNA_split<br><br>listP <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>n <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>test_s<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    test <span class="hljs-operator">=</span> as.matrix<span class="hljs-punctuation">(</span>f_br_cluster<span class="hljs-punctuation">(</span>test_s<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Region&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;hM1_hmca_class&#x27;</span><span class="hljs-punctuation">,</span> lc_prop <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    hc <span class="hljs-operator">&lt;-</span> f_hc<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span><br>    cop <span class="hljs-operator">&lt;-</span> paste<span class="hljs-punctuation">(</span>n<span class="hljs-punctuation">,</span> hc <span class="hljs-operator">%&gt;%</span> f_hc_cop<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>cop<span class="hljs-punctuation">)</span><br>    listP<span class="hljs-punctuation">[[</span>n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-punctuation">(</span>f_hc<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_ggdendrogram<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_ggplot2_ti<span class="hljs-punctuation">(</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;hclust by proportion of cells in &#x27;</span><span class="hljs-punctuation">,</span> n<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> subtitle <span class="hljs-operator">=</span> cop<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    <span class="hljs-punctuation">(</span>f_corrplot<span class="hljs-punctuation">(</span>test<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> f_ggplot2_ti<span class="hljs-punctuation">(</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;cor by proportion of cells of &#x27;</span><span class="hljs-punctuation">,</span> n<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="第五步-输出计算结果"><a href="#第五步-输出计算结果" class="headerlink" title="第五步 输出计算结果"></a>第五步 输出计算结果</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"><span class="hljs-comment"># 配置数据和mark基因表的路径</span><br>root_path <span class="hljs-operator">=</span> <span class="hljs-string">&quot;~/zlliu/R_data/hBLA&quot;</span><br> <br><span class="hljs-comment"># 配置结果保存路径</span><br>output_path <span class="hljs-operator">=</span> <span class="hljs-string">&quot;~/zlliu/R_output/21.12.17.pcell_hclust&quot;</span><br><span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>file.exists<span class="hljs-punctuation">(</span>output_path<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>dir.create<span class="hljs-punctuation">(</span>output_path<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br> <br><span class="hljs-comment"># 设置工作目录，输出文件将保存在此目录下</span><br>setwd<span class="hljs-punctuation">(</span>output_path<span class="hljs-punctuation">)</span><br>getwd<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><br>library<span class="hljs-punctuation">(</span>export<span class="hljs-punctuation">)</span><br>f_ppt_output <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>fileName<span class="hljs-punctuation">,</span> image<span class="hljs-punctuation">,</span> lc_aspectr<span class="hljs-operator">=</span><span class="hljs-number">1.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>p <span class="hljs-keyword">in</span> image<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        graph2ppt<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>p<span class="hljs-punctuation">,</span> file<span class="hljs-operator">=</span>fileName<span class="hljs-punctuation">,</span> width<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> aspectr<span class="hljs-operator">=</span>lc_aspectr<span class="hljs-punctuation">,</span> append <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> vector.graphic<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br><span class="hljs-punctuation">&#125;</span><br><br>f_ppt_output<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;split.pptx&#x27;</span><span class="hljs-punctuation">,</span> listP<span class="hljs-punctuation">,</span> lc_aspectr <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br>f_ppt_output<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;sc_Neuron.pptx&#x27;</span><span class="hljs-punctuation">,</span> listPN<span class="hljs-punctuation">,</span> lc_aspectr <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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