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            <h1 id="seo-header">基于NMF分解的降维聚类</h1>
            
            
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                <h2 id="安装补充包"><a href="#安装补充包" class="headerlink" title="安装补充包"></a>安装补充包</h2><ul>
<li><a target="_blank" rel="noopener" href="https://occdn.limour.top/2366.html">conda activate seurat</a></li>
<li>conda install -c conda-forge r-nmf -y</li>
<li>conda install -c conda-forge r-fastica -y</li>
</ul>
<h2 id="获取非负表达矩阵"><a href="#获取非负表达矩阵" class="headerlink" title="获取非负表达矩阵"></a>获取非负表达矩阵</h2><p>使用<a target="_blank" rel="noopener" href="https://occdn.limour.top/2369.html">《使用DoubletFinder标注Doublet》</a>中的数据</p>
<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></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;SRX8890106.rds&#x27;</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">@</span>meta.data <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;SRX8890106_meta.rds&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 某个群进行细分</span><br>sce <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> seurat_clusters <span class="hljs-operator">==</span> <span class="hljs-number">6</span> <br>              <span class="hljs-operator">&amp;</span> DF.classifications_0.25_0.04_416 <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;Singlet&#x27;</span><span class="hljs-punctuation">)</span><br><span class="hljs-comment"># 取项目子集后重新标准化</span><br>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> assay <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;RNA&#x27;</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-string">&quot;percent.rp&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><span class="hljs-comment"># Seurat::PrepSCTFindMarkers</span><br><span class="hljs-comment"># 获取非负矩阵</span><br>DefaultAssay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;RNA&#x27;</span><br>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>sce <span class="hljs-operator">&lt;-</span> Seurat<span class="hljs-operator">::</span>ScaleData<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> do.center <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> <span class="hljs-comment"># NMF 要求非负矩阵</span><br><span class="hljs-comment">#                          vars.to.regress = c(&quot;CC.Difference&quot;, &quot;percent.mt&quot;, &quot;percent.rp&quot;),</span><br>                         features <span class="hljs-operator">=</span> Seurat<span class="hljs-operator">::</span>VariableFeatures<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> assay <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;SCT&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>vm <span class="hljs-operator">&lt;-</span> sce<span class="hljs-punctuation">[[</span>Seurat<span class="hljs-operator">::</span>DefaultAssay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-operator">@</span>scale.data<br></code></pre></td></tr></table></figure>

<h2 id="NMF分解聚类"><a href="#NMF分解聚类" class="headerlink" title="NMF分解聚类"></a>NMF分解聚类</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">saveRDS<span class="hljs-punctuation">(</span>vm<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;vm.rds&#x27;</span><span class="hljs-punctuation">)</span><br>vm <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;vm.rds&#x27;</span><span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>NMF<span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> NMF<span class="hljs-operator">::</span>nmf<span class="hljs-punctuation">(</span>vm<span class="hljs-punctuation">,</span> <span class="hljs-number">2</span><span class="hljs-operator">:</span><span class="hljs-number">7</span><span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;snmf/r&quot;</span><span class="hljs-punctuation">,</span> seed<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ica&#x27;</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br><span class="hljs-comment">## 更推荐使用Seurat的分群走向判断分群数量</span><br></code></pre></td></tr></table></figure>

<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></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>NMF<span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> NMF<span class="hljs-operator">::</span>nmf<span class="hljs-punctuation">(</span>vm<span class="hljs-punctuation">,</span> <span class="hljs-number">4</span><span class="hljs-punctuation">,</span> method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;snmf/r&quot;</span><span class="hljs-punctuation">,</span> seed <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;ica&#x27;</span><span class="hljs-punctuation">)</span> <br>DefaultAssay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;SCT&#x27;</span><br>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>sce<span class="hljs-operator">@</span>reductions<span class="hljs-operator">$</span>nmf <span class="hljs-operator">&lt;-</span> sce<span class="hljs-operator">@</span>reductions<span class="hljs-operator">$</span>pca<br>sce<span class="hljs-operator">@</span>reductions<span class="hljs-operator">$</span>nmf<span class="hljs-operator">@</span>cell.embeddings <span class="hljs-operator">&lt;-</span> t<span class="hljs-punctuation">(</span>coef<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>    <br>sce<span class="hljs-operator">@</span>reductions<span class="hljs-operator">$</span>nmf<span class="hljs-operator">@</span>feature.loadings <span class="hljs-operator">&lt;-</span> basis<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <br>sce <span class="hljs-operator">&lt;-</span> RunUMAP<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> reduction <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;nmf&#x27;</span><span class="hljs-punctuation">,</span> dims <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 和分群数量一致</span><br>group <span class="hljs-operator">&lt;-</span> predict<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">$</span>nmf_group <span class="hljs-operator">&lt;-</span> group<span class="hljs-punctuation">[</span>colnames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width <span class="hljs-operator">=</span> <span class="hljs-number">6</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>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> label <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> repel <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br>        group.by <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;nmf_group&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

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<h2 id="提取signatures"><a href="#提取signatures" class="headerlink" title="提取signatures"></a><strong>提取</strong>signatures</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">coefmap<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>consensusmap<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 可能要设置nrun才有?</span><br>df <span class="hljs-operator">&lt;-</span> extractFeatures<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> <span class="hljs-number">20L</span><span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> lapply<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>x<span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>do.call<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;rbind&quot;</span><span class="hljs-punctuation">,</span> df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>df<br></code></pre></td></tr></table></figure>
                
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