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  136. <h1 id="seo-header">使用SCTransform标准化</h1>
  137. <div class="markdown-body">
  138. <h2 id="安装包"><a href="#安装包" class="headerlink" title="安装包"></a>安装包</h2><ul>
  139. <li>conda create -n seurat -c conda-forge r-seurat&#x3D;4.1.1 -y</li>
  140. <li>conda activate seurat</li>
  141. <li>conda install -c conda-forge r-tidyverse -y</li>
  142. <li>conda install -c conda-forge r-irkernel -y</li>
  143. <li>Rscript -e “IRkernel::installspec(name&#x3D;’seurat’, displayname&#x3D;’r-seurat’)”</li>
  144. <li>conda install -c conda-forge r-biocmanager -y</li>
  145. <li># conda install -c conda-forge r-sctransform -y</li>
  146. <li># conda install -c conda-forge r-rocr -y</li>
  147. <li>conda install -c conda-forge r-modes -y</li>
  148. <li># conda install -c conda-forge r-kernsmooth -y</li>
  149. <li>conda install -c conda-forge r-fields -y</li>
  150. <li>conda install -c conda-forge r-devtools -y</li>
  151. <li>conda install -c conda-forge r-clustree -y</li>
  152. <li>BiocManager::install(“glmGamPoi”)</li>
  153. <li>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</li>
  154. <li>wget -e “https_proxy&#x3D;<a target="_blank" rel="noopener" href="http://127.0.0.1:20809/">http://127.0.0.1:20809</a>“ <a target="_blank" rel="noopener" href="https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip">https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip</a> -O DoubletFinder-master.zip</li>
  155. <li>devtools::install_local(‘DoubletFinder-master.zip’)</li>
  156. </ul>
  157. <h2 id="读取数据"><a href="#读取数据" class="headerlink" title="读取数据"></a>读取数据</h2><h3 id="从UMI矩阵"><a href="#从UMI矩阵" class="headerlink" title="从UMI矩阵"></a>从UMI矩阵</h3><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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> read.table<span class="hljs-punctuation">(</span>gzfile<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;GSM4203181_data.matrix.txt.gz&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <br> header <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CreateSeuratObject<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;GSM4203181&#x27;</span><span class="hljs-punctuation">,</span><br> min.cells <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> min.features <span class="hljs-operator">=</span> <span class="hljs-number">200</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^MT-&quot;</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.ERCC&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^ERCC-&quot;</span><span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>sce<span class="hljs-operator">@</span>meta.data<span class="hljs-punctuation">)</span><br>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;orig.ident&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;sample&#x27;</span><span class="hljs-punctuation">,</span> substr<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span><span class="hljs-number">18</span><span class="hljs-punctuation">,</span>nchar<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>table<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;orig.ident&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">@</span>meta.data<br>saveRDS<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;GSM4203181.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  158. <h3 id="cellranger输出"><a href="#cellranger输出" class="headerlink" title="cellranger输出"></a>cellranger输出</h3><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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>Read10X<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;filtered_feature_bc_matrix&#x27;</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CreateSeuratObject<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> project <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;SRX6887740&#x27;</span><span class="hljs-punctuation">,</span><br> min.cells <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">,</span> min.features <span class="hljs-operator">=</span> <span class="hljs-number">200</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^MT-&quot;</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.ERCC&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>PercentageFeatureSet<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^ERCC-&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  159. <h2 id="初步QC"><a href="#初步QC" class="headerlink" title="初步QC"></a>初步QC</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></pre></td><td class="code"><pre><code class="hljs R">options<span class="hljs-punctuation">(</span>repr.plot.width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">)</span><br>Seurat<span class="hljs-operator">::</span>VlnPlot<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;nFeature_RNA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;nCount_RNA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br>plot1 <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>FeatureScatter<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> feature1 <span class="hljs-operator">=</span> <span class="hljs-string">&quot;nCount_RNA&quot;</span><span class="hljs-punctuation">,</span> feature2 <span class="hljs-operator">=</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">)</span><br>plot2 <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>FeatureScatter<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> feature1 <span class="hljs-operator">=</span> <span class="hljs-string">&quot;nCount_RNA&quot;</span><span class="hljs-punctuation">,</span> feature2 <span class="hljs-operator">=</span> <span class="hljs-string">&quot;nFeature_RNA&quot;</span><span class="hljs-punctuation">)</span><br>plot1 <span class="hljs-operator">+</span> plot2<br>sce <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> nFeature_RNA <span class="hljs-operator">&gt;</span> <span class="hljs-number">2500</span> <span class="hljs-operator">&amp;</span> nFeature_RNA <span class="hljs-operator">&lt;</span> <span class="hljs-number">7500</span> <span class="hljs-operator">&amp;</span> nCount_RNA <span class="hljs-operator">&gt;</span> <span class="hljs-number">2500</span> <span class="hljs-operator">&amp;</span> nCount_RNA <span class="hljs-operator">&lt;</span> <span class="hljs-number">50000</span> <span class="hljs-operator">&amp;</span> percent.mt <span class="hljs-operator">&lt;</span> <span class="hljs-number">7.5</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  160. <h3 id="计算细胞周期评分"><a href="#计算细胞周期评分" class="headerlink" title="计算细胞周期评分"></a>计算细胞周期评分</h3><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">sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>NormalizeData<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><br>g2m_genes <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CaseMatch<span class="hljs-punctuation">(</span>search<span class="hljs-operator">=</span>Seurat<span class="hljs-operator">::</span>cc.genes<span class="hljs-operator">$</span>g2m.genes<span class="hljs-punctuation">,</span> <br> match<span class="hljs-operator">=</span>rownames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>s_genes <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CaseMatch<span class="hljs-punctuation">(</span>search<span class="hljs-operator">=</span>Seurat<span class="hljs-operator">::</span>cc.genes<span class="hljs-operator">$</span>s.genes<span class="hljs-punctuation">,</span> <br> match<span class="hljs-operator">=</span>rownames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>CellCycleScoring<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> g2m.features<span class="hljs-operator">=</span>g2m_genes<span class="hljs-punctuation">,</span> s.features<span class="hljs-operator">=</span>s_genes<span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">$</span>CC.Difference <span class="hljs-operator">&lt;-</span> sce<span class="hljs-operator">$</span>S.Score <span class="hljs-operator">-</span> sce<span class="hljs-operator">$</span>G2M.Score<br></code></pre></td></tr></table></figure>
  161. <h2 id="SCTransform标准化"><a href="#SCTransform标准化" class="headerlink" title="SCTransform标准化"></a>SCTransform标准化</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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>SCTransform<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> vst.flavor <span class="hljs-operator">=</span> <span class="hljs-string">&quot;v2&quot;</span><span class="hljs-punctuation">,</span><br> vars.to.regress <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;CC.Difference&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> verbose <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  162. <h2 id="查看分群走向"><a href="#查看分群走向" class="headerlink" title="查看分群走向"></a>查看分群走向</h2><h3 id="降维"><a href="#降维" class="headerlink" title="降维"></a>降维</h3><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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>RunPCA<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> assay<span class="hljs-operator">=</span><span class="hljs-string">&quot;SCT&quot;</span><span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>Seurat<span class="hljs-operator">::</span>ElbowPlot<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> ndims <span class="hljs-operator">=</span> <span class="hljs-number">50</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>RunUMAP<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;pca&quot;</span><span class="hljs-punctuation">,</span> <br> dims <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>FindNeighbors<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;pca&quot;</span><span class="hljs-punctuation">,</span> <br> dims <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span> verbose <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  163. <h3 id="分群"><a href="#分群" class="headerlink" title="分群"></a>分群</h3><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">sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>FindClusters<span class="hljs-punctuation">(</span><br> object <span class="hljs-operator">=</span> sce<span class="hljs-punctuation">,</span><br> resolution <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>seq<span class="hljs-punctuation">(</span><span class="hljs-number">.1</span><span class="hljs-punctuation">,</span><span class="hljs-number">1.6</span><span class="hljs-punctuation">,</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#起始粒度,结束粒度,间隔</span><br><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>clustree<span class="hljs-punctuation">)</span><br>clustree<span class="hljs-operator">::</span>clustree<span class="hljs-punctuation">(</span>sce<span class="hljs-operator">@</span>meta.data<span class="hljs-punctuation">,</span> prefix <span class="hljs-operator">=</span> <span class="hljs-string">&quot;SCT_snn_res.&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  164. <p><img src="https://img-cdn.limour.top/2022/09/28/63346be4bd300.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></p>
  165. <p>这图还挺好看的</p>
  166. <h2 id="使用DoubletFinder去除doublet"><a href="#使用DoubletFinder去除doublet" class="headerlink" title="使用DoubletFinder去除doublet"></a>使用DoubletFinder去除doublet</h2><h3 id="pK-Identification"><a href="#pK-Identification" class="headerlink" title="pK Identification"></a>pK Identification</h3><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></pre></td><td class="code"><pre><code class="hljs R">sweep.res <span class="hljs-operator">&lt;-</span> DoubletFinder<span class="hljs-operator">::</span>paramSweep_v3<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> PCs <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">10</span><span class="hljs-punctuation">,</span> sct <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> num.cores<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><br>sweep.stats <span class="hljs-operator">&lt;-</span> DoubletFinder<span class="hljs-operator">::</span>summarizeSweep<span class="hljs-punctuation">(</span>sweep.res<span class="hljs-punctuation">,</span> GT <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>bcmvn <span class="hljs-operator">&lt;-</span> DoubletFinder<span class="hljs-operator">::</span>find.pK<span class="hljs-punctuation">(</span>sweep.stats<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  167. <h3 id="Run-DoubletFinder"><a href="#Run-DoubletFinder" class="headerlink" title="Run DoubletFinder"></a>Run DoubletFinder</h3><p><img src="https://img-cdn.limour.top/2022/09/29/633471b0dea83.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></p>
  168. <p><strong><a target="_blank" rel="noopener" href="https://cloud.tencent.com/developer/article/1825672">10X genomics单细胞平台的dulblets比率</a></strong></p>
  169. <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></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment">## Assuming 1.6% doublet formation rate - tailor for your dataset</span><br>nExp_poi <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span><span class="hljs-number">0.016</span><span class="hljs-operator">*</span>nrow<span class="hljs-punctuation">(</span>sce<span class="hljs-operator">@</span>meta.data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>pK_bcmvn <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>bcmvn<span class="hljs-operator">$</span>pK<span class="hljs-punctuation">[</span>which.max<span class="hljs-punctuation">(</span>bcmvn<span class="hljs-operator">$</span>BCmetric<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> DoubletFinder<span class="hljs-operator">::</span>doubletFinder_v3<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> PCs <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">10</span><span class="hljs-punctuation">,</span> <br> pN <span class="hljs-operator">=</span> <span class="hljs-number">0.25</span><span class="hljs-punctuation">,</span> pK <span class="hljs-operator">=</span> pK_bcmvn<span class="hljs-punctuation">,</span> <br> nExp <span class="hljs-operator">=</span> nExp_poi<span class="hljs-punctuation">,</span> reuse.pANN <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">,</span> <br> sct <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">@</span>meta.data<br>DimPlot<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;umap&quot;</span><span class="hljs-punctuation">,</span> group.by <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;DF.classifications_0.25_0.2_20&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  170. <figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> DF.classifications_0.25_0.2_20 <span class="hljs-operator">!=</span> <span class="hljs-string">&#x27;Doublet&#x27;</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;SRX6887740.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
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  252. Fluid.utils.waitElementVisible('#waline .vcontent', () => {
  253. var imgSelector = '#waline .vcontent img:not(.vemoji)';
  254. Fluid.plugins.imageCaption(imgSelector);
  255. Fluid.plugins.fancyBox(imgSelector);
  256. })
  257. });
  258. });
  259. </script>
  260. <noscript>Please enable JavaScript to view the comments</noscript>
  261. </article>
  262. </article>
  263. </div>
  264. </div>
  265. </div>
  266. <div class="side-col d-none d-lg-block col-lg-2">
  267. <aside class="sidebar" style="margin-left: -1rem">
  268. <div id="toc">
  269. <p class="toc-header">
  270. <i class="iconfont icon-list"></i>
  271. <span>Table of Contents</span>
  272. </p>
  273. <div class="toc-body" id="toc-body"></div>
  274. </div>
  275. </aside>
  276. </div>
  277. </div>
  278. </div>
  279. <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
  280. <i class="iconfont icon-arrowup" aria-hidden="true"></i>
  281. </a>
  282. <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
  283. aria-hidden="true">
  284. <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
  285. <div class="modal-content">
  286. <div class="modal-header text-center">
  287. <h4 class="modal-title w-100 font-weight-bold">Search</h4>
  288. <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
  289. <span aria-hidden="true">&times;</span>
  290. </button>
  291. </div>
  292. <div class="modal-body mx-3">
  293. <div class="md-form mb-5">
  294. <input type="text" id="local-search-input" class="form-control validate">
  295. <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
  296. </div>
  297. <div class="list-group" id="local-search-result"></div>
  298. </div>
  299. </div>
  300. </div>
  301. </div>
  302. </main>
  303. <footer>
  304. <div class="footer-inner">
  305. <div class="footer-content">
  306. <a target="_blank" rel="nofollow noopener" href="http://www.beian.gov.cn/portal/registerSystemInfo?recordcode=43130202000203"><img src="https://img.limour.top/2023/08/27/64eadeb81d6a0.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload>湘公网安备 43130202000203号 </a> <a target="_blank" rel="nofollow noopener" href="https://beian.miit.gov.cn/">湘ICP备20008299号 </a> <a target="_blank" rel="nofollow noopener" href="https://icp.gov.moe/?keyword=20210128">萌ICP备20210128号</a> <br> <a href="https://www.foreverblog.cn/" target="_blank"> <img src="https://img.foreverblog.cn/logo_en_default.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="" style="width:auto;height:24px"> </a> <br> <a href="https://hexo.io" target="_blank" rel="nofollow noopener"><span>Hexo</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/fluid-dev/hexo-theme-fluid" target="_blank" rel="nofollow noopener"><span>Fluid</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/limour-blog/archives-occdn" target="_blank" rel="nofollow noopener"><span>SRC</span></a>
  307. </div>
  308. </div>
  309. </footer>
  310. <!-- Scripts -->
  311. <script src="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.js" ></script>
  312. <link rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />
  313. <script>
  314. NProgress.configure({"showSpinner":false,"trickleSpeed":100})
  315. NProgress.start()
  316. window.addEventListener('load', function() {
  317. NProgress.done();
  318. })
  319. </script>
  320. <script src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
  321. <script src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
  322. <script src="/js/events.js" ></script>
  323. <script src="/js/plugins.js" ></script>
  324. <script src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  325. <script>
  326. (function (window, document) {
  327. var typing = Fluid.plugins.typing;
  328. var subtitle = document.getElementById('subtitle');
  329. if (!subtitle || !typing) {
  330. return;
  331. }
  332. var text = subtitle.getAttribute('data-typed-text');
  333. typing(text);
  334. })(window, document);
  335. </script>
  336. <script src="/js/img-lazyload.js" ></script>
  337. <script>
  338. Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
  339. var toc = jQuery('#toc');
  340. if (toc.length === 0 || !window.tocbot) { return; }
  341. var boardCtn = jQuery('#board-ctn');
  342. var boardTop = boardCtn.offset().top;
  343. window.tocbot.init(Object.assign({
  344. tocSelector : '#toc-body',
  345. contentSelector : '.markdown-body',
  346. linkClass : 'tocbot-link',
  347. activeLinkClass : 'tocbot-active-link',
  348. listClass : 'tocbot-list',
  349. isCollapsedClass: 'tocbot-is-collapsed',
  350. collapsibleClass: 'tocbot-is-collapsible',
  351. scrollSmooth : true,
  352. includeTitleTags: true,
  353. headingsOffset : -boardTop,
  354. }, CONFIG.toc));
  355. if (toc.find('.toc-list-item').length > 0) {
  356. toc.css('visibility', 'visible');
  357. }
  358. Fluid.events.registerRefreshCallback(function() {
  359. if ('tocbot' in window) {
  360. tocbot.refresh();
  361. var toc = jQuery('#toc');
  362. if (toc.length === 0 || !tocbot) {
  363. return;
  364. }
  365. if (toc.find('.toc-list-item').length > 0) {
  366. toc.css('visibility', 'visible');
  367. }
  368. }
  369. });
  370. });
  371. </script>
  372. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  373. <script>Fluid.plugins.codeWidget();</script>
  374. <script>
  375. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  376. window.anchors.options = {
  377. placement: CONFIG.anchorjs.placement,
  378. visible : CONFIG.anchorjs.visible
  379. };
  380. if (CONFIG.anchorjs.icon) {
  381. window.anchors.options.icon = CONFIG.anchorjs.icon;
  382. }
  383. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  384. var res = [];
  385. for (var item of el) {
  386. res.push('.markdown-body > ' + item.trim());
  387. }
  388. if (CONFIG.anchorjs.placement === 'left') {
  389. window.anchors.options.class = 'anchorjs-link-left';
  390. }
  391. window.anchors.add(res.join(', '));
  392. Fluid.events.registerRefreshCallback(function() {
  393. if ('anchors' in window) {
  394. anchors.removeAll();
  395. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  396. var res = [];
  397. for (var item of el) {
  398. res.push('.markdown-body > ' + item.trim());
  399. }
  400. if (CONFIG.anchorjs.placement === 'left') {
  401. anchors.options.class = 'anchorjs-link-left';
  402. }
  403. anchors.add(res.join(', '));
  404. }
  405. });
  406. });
  407. </script>
  408. <script>
  409. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  410. Fluid.plugins.fancyBox();
  411. });
  412. </script>
  413. <script>Fluid.plugins.imageCaption();</script>
  414. <script src="/js/local-search.js" ></script>
  415. <!-- 主题的启动项,将它保持在最底部 -->
  416. <!-- the boot of the theme, keep it at the bottom -->
  417. <script src="/js/boot.js" ></script>
  418. <noscript>
  419. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  420. </noscript>
  421. <!-- hexo injector body_end start -->
  422. <script defer src="/theme-inject/timeliness.js"></script>
  423. <!-- hexo injector body_end end --></body>
  424. </html>