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            <h1 id="seo-header">【迁移】CellTypist 注释免疫细胞亚群</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <h2 id="安装-CellTypist">安装 CellTypist</h2>
<ul>
<li><a href="/-ji-lu--an-zhuang-sheng-xin-de-dai-ma-bian-xie-huan-jing">配置环境</a></li>
</ul>
<figure class="highlight bash"><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><span class="line">conda create -n celltypist -c conda-forge r-base=4.1.2</span><br><span class="line">conda activate celltypist</span><br><span class="line">conda install -c conda-forge r-seurat=4.1.0 -y</span><br><span class="line">conda install -c conda-forge r-irkernel=1.3 -y</span><br><span class="line">IRkernel::installspec(name=<span class="string">&#x27;celltypist&#x27;</span>, displayname=<span class="string">&#x27;r-celltypist&#x27;</span>)</span><br><span class="line">conda install -c conda-forge scanpy=1.8.2 -y</span><br><span class="line">/opt/conda/envs/celltypist/bin/pip3 install celltypist -i https://pypi.tuna.tsinghua.edu.cn/simple</span><br><span class="line">conda install -c conda-forge r-reticulate=1.24 -y</span><br><span class="line">python3</span><br><span class="line">import celltypist</span><br><span class="line">celltypist.models.download_models(force_update = False)</span><br></pre></td></tr></table></figure>
<h2 id="加载包">加载包</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></pre></td><td class="code"><pre><span class="line">Sys.setenv<span class="punctuation">(</span>RETICULATE_PYTHON <span class="operator">=</span> <span class="string">&quot;/opt/conda/envs/celltypist/bin/python3.8&quot;</span><span class="punctuation">)</span></span><br><span class="line">library<span class="punctuation">(</span>reticulate<span class="punctuation">)</span></span><br><span class="line">scanpy <span class="operator">=</span> import<span class="punctuation">(</span><span class="string">&quot;scanpy&quot;</span><span class="punctuation">)</span></span><br><span class="line">celltypist <span class="operator">=</span> import<span class="punctuation">(</span><span class="string">&quot;celltypist&quot;</span><span class="punctuation">)</span></span><br><span class="line">pandas <span class="operator">&lt;-</span> import<span class="punctuation">(</span><span class="string">&quot;pandas&quot;</span><span class="punctuation">)</span></span><br><span class="line">numpy <span class="operator">=</span> import<span class="punctuation">(</span><span class="string">&quot;numpy&quot;</span><span class="punctuation">)</span></span><br><span class="line">py_config<span class="punctuation">(</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="加载数据">加载数据</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></pre></td><td class="code"><pre><span class="line">library<span class="punctuation">(</span>Seurat<span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> readRDS<span class="punctuation">(</span><span class="string">&quot;~/upload/yy_zhang_data/scRNA-seq/pca.celltype.rds&quot;</span><span class="punctuation">)</span></span><br><span class="line">Myeloid <span class="operator">&lt;-</span> subset<span class="punctuation">(</span>sce<span class="punctuation">,</span> cell_type<span class="operator">==</span><span class="string">&#x27;Myeloid&#x27;</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="seurat-转-scanpy">seurat 转 scanpy</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></pre></td><td class="code"><pre><span class="line"><span class="comment"># 数据矩阵, scanpy与Seurat的行列定义相反</span></span><br><span class="line">adata.X <span class="operator">=</span> numpy<span class="operator">$</span>array<span class="punctuation">(</span>t<span class="punctuation">(</span>as.matrix<span class="punctuation">(</span>Myeloid<span class="punctuation">[[</span><span class="string">&#x27;RNA&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span><span class="operator">@</span>counts<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"><span class="comment"># 对每个细胞的观察</span></span><br><span class="line">adata.obs <span class="operator">=</span> pandas<span class="operator">$</span>DataFrame<span class="punctuation">(</span>Myeloid<span class="operator">@</span>meta.data<span class="punctuation">[</span>colnames<span class="punctuation">(</span>Myeloid<span class="punctuation">[[</span><span class="string">&#x27;RNA&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span><span class="operator">@</span>counts<span class="punctuation">)</span><span class="punctuation">,</span><span class="punctuation">]</span><span class="punctuation">)</span></span><br><span class="line"><span class="comment"># 对基因矩阵的注释</span></span><br><span class="line">adata.var <span class="operator">=</span> pandas<span class="operator">$</span>DataFrame<span class="punctuation">(</span>data.frame<span class="punctuation">(</span>gene <span class="operator">=</span> rownames<span class="punctuation">(</span>Myeloid<span class="punctuation">[[</span><span class="string">&#x27;RNA&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span><span class="operator">@</span>counts<span class="punctuation">)</span><span class="punctuation">,</span> row.names <span class="operator">=</span> rownames<span class="punctuation">(</span>Myeloid<span class="punctuation">[[</span><span class="string">&#x27;RNA&#x27;</span><span class="punctuation">]</span><span class="punctuation">]</span><span class="operator">@</span>counts<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line"><span class="comment"># 组装AnnData对象</span></span><br><span class="line">adata <span class="operator">=</span> scanpy<span class="operator">$</span>AnnData<span class="punctuation">(</span>X <span class="operator">=</span> adata.X<span class="punctuation">,</span> obs<span class="operator">=</span>adata.obs<span class="punctuation">,</span> var<span class="operator">=</span>adata.var<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="进行预测">进行预测</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></pre></td><td class="code"><pre><span class="line">model <span class="operator">=</span> celltypist<span class="operator">$</span>models<span class="operator">$</span>Model<span class="operator">$</span>load<span class="punctuation">(</span>model <span class="operator">=</span> <span class="string">&#x27;Immune_All_AddPIP.pkl&#x27;</span><span class="punctuation">)</span></span><br><span class="line">model<span class="operator">$</span>cell_types</span><br><span class="line">scanpy<span class="operator">$</span>pp<span class="operator">$</span>normalize_total<span class="punctuation">(</span>adata<span class="punctuation">,</span> target_sum<span class="operator">=</span><span class="number">1e4</span><span class="punctuation">)</span></span><br><span class="line">scanpy<span class="operator">$</span>pp<span class="operator">$</span>log1p<span class="punctuation">(</span>adata<span class="punctuation">)</span></span><br><span class="line">predictions <span class="operator">=</span> celltypist<span class="operator">$</span>annotate<span class="punctuation">(</span>adata<span class="punctuation">,</span> model <span class="operator">=</span> <span class="string">&#x27;Immune_All_AddPIP.pkl&#x27;</span><span class="punctuation">,</span> majority_voting <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="预测添加到-seurat-对象">预测添加到 seurat 对象</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><span class="line">Myeloid <span class="operator">=</span> AddMetaData<span class="punctuation">(</span>Myeloid<span class="punctuation">,</span> predictions<span class="operator">$</span>predicted_labels<span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
                
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