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            <h1 id="seo-header">【复习】单细胞最佳实践的流程</h1>
            
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                    Last updated on March 19, 2024 pm
                  
                
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                <h2 id="配置环境">配置环境</h2>
<ul>
<li><a href="/-ji-lu--an-zhuang-sheng-xin-de-dai-ma-bian-xie-huan-jing">基础编程环境</a></li>
<li><a href="/-fu-ke-GitHub-wen-jian-jia-su">GitHub 下载加速</a></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></pre></td><td class="code"><pre><span class="line">options<span class="punctuation">(</span>BioC_mirror<span class="operator">=</span><span class="string">&quot;https://mirrors.ustc.edu.cn/bioc/&quot;</span><span class="punctuation">)</span> <span class="comment">## 指定 BiocManager::install 镜像</span></span><br><span class="line">options<span class="punctuation">(</span><span class="string">&quot;repos&quot;</span> <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span>CRAN<span class="operator">=</span><span class="string">&quot;https://mirrors.tuna.tsinghua.edu.cn/CRAN/&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span> <span class="comment">## 指定 install.packages 镜像，</span></span><br><span class="line">options<span class="punctuation">(</span>ggrepel.max.overlaps <span class="operator">=</span> <span class="literal">Inf</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<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><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></pre></td><td class="code"><pre><span class="line">nano ~/.Rprofile <span class="comment"># 内容如上，配置镜像</span></span><br><span class="line">conda create -n seurat5 -c conda-forge r-seurat=4.3.0 -y</span><br><span class="line">conda activate seurat5</span><br><span class="line">conda install -c conda-forge r-irkernel -y</span><br><span class="line">conda install -c conda-forge r-devtools -y</span><br><span class="line">conda install -c conda-forge r-biocmanager -y</span><br><span class="line">conda install -c conda-forge r-tidyverse -y</span><br><span class="line">conda install -c conda-forge r-clustree -y</span><br><span class="line">Rscript -e <span class="string">&quot;IRkernel::installspec(name=&#x27;seurat5&#x27;, displayname=&#x27;seurat5&#x27;)&quot;</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 开始 seurat5 的安装</span></span><br><span class="line">wget https://github.com/satijalab/seurat/archive/refs/heads/seurat5.zip -O seurat5.zip</span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;seurat5.zip&#x27;)&quot;</span></span><br><span class="line"><span class="comment">## Rscript -e &quot;devtools::install_local(&#x27;seurat5.zip&#x27;, host = &#x27;xxx.limour.top/token/api.github.com&#x27;)&quot;</span></span><br><span class="line"><span class="comment">## options(Seurat.object.assay.version = &#x27;v5&#x27;) 使用 seurat5</span></span><br><span class="line">conda install -c conda-forge hdf5 -y</span><br><span class="line">wget https://github.com/bnprks/BPCells/archive/refs/heads/main.zip -O BPCells.zip</span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;BPCells.zip&#x27;)&quot;</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 开始 DoubletFinder 的安装</span></span><br><span class="line">wget https://github.com/chris-mcginnis-ucsf/DoubletFinder/archive/refs/heads/master.zip -O DoubletFinder.zip</span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;DoubletFinder.zip&#x27;)&quot;</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 开始 decontX 的安装</span></span><br><span class="line">wget https://github.com/campbio/decontX/archive/refs/heads/main.zip -O decontX.zip</span><br><span class="line">conda install -c conda-forge imagemagick -y</span><br><span class="line">conda install -c conda-forge r-ggrastr -y</span><br><span class="line">Rscript -e <span class="string">&#x27;BiocManager::install(&quot;celda&quot;)&#x27;</span></span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;decontX.zip&#x27;)&quot;</span></span><br><span class="line"><span class="comment">## api.github.com 错误就换用下面的命令</span></span><br><span class="line"><span class="comment"># Rscript -e &#x27;remotes::install_local(&quot;decontX.zip&quot;, repos = NULL, type = &quot;source&quot;)&#x27;</span></span><br><span class="line"><span class="comment"># Rscript -e &quot;devtools::install_local(&#x27;decontX.zip&#x27;, repos = NULL, type=&#x27;source&#x27;)&quot;</span></span><br><span class="line"><span class="comment"># Rscript -e &#x27;install.packages(&quot;decontX.zip&quot;, repos = NULL, type = &quot;source&quot;)&#x27;</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 开始 plot1cell 的安装</span></span><br><span class="line">wget https://github.com/mojaveazure/loomR/archive/refs/heads/master.zip -O loomR.zip</span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;loomR.zip&#x27;)&quot;</span></span><br><span class="line">wget https://github.com/HaojiaWu/plot1cell/archive/refs/heads/master.zip -O plot1cell.zip</span><br><span class="line">Rscript -e <span class="string">&#x27;BiocManager::install(c(&quot;biomaRt&quot;,&quot;EnsDb.Hsapiens.v86&quot;,&quot;GEOquery&quot;,&quot;simplifyEnrichment&quot;))&#x27;</span></span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;plot1cell.zip&#x27;)&quot;</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 开始 SCTransform 的安装</span></span><br><span class="line">Rscript -e <span class="string">&#x27;BiocManager::install(&quot;glmGamPoi&quot;)&#x27;</span></span><br></pre></td></tr></table></figure>
<h3 id="附加-安装SCP">附加 安装SCP</h3>
<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><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></pre></td><td class="code"><pre><span class="line">conda create -n r-scp -c conda-forge r -y</span><br><span class="line">conda activate r-scp</span><br><span class="line">conda install -c conda-forge r-irkernel -y</span><br><span class="line">conda install -c conda-forge r-devtools -y</span><br><span class="line">conda install -c conda-forge r-biocmanager -y</span><br><span class="line">Rscript -e <span class="string">&quot;IRkernel::installspec(name=&#x27;r-scp&#x27;, displayname=&#x27;r-scp&#x27;)&quot;</span></span><br><span class="line"><span class="comment">## 开始 SCP 的安装</span></span><br><span class="line">wget https://github.com/zhanghao-njmu/SCP/archive/refs/heads/main.zip -O SCP.zip</span><br><span class="line">conda install -c conda-forge r-ggplot2 -y</span><br><span class="line">conda install -c conda-forge r-gridgraphics -y</span><br><span class="line">Rscript -e <span class="string">&#x27;BiocManager::install(&quot;ggtree&quot;)&#x27;</span></span><br><span class="line">Rscript -e <span class="string">&quot;devtools::install_local(&#x27;SCP.zip&#x27;)&quot;</span></span><br><span class="line"></span><br><span class="line"><span class="comment">## 找到 conda 的路径</span></span><br><span class="line">whereis conda</span><br><span class="line"><span class="comment"># /opt/conda/bin/conda</span></span><br></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></pre></td><td class="code"><pre><span class="line"><span class="comment">## 创建 SCP 的 python 环境</span></span><br><span class="line">options<span class="punctuation">(</span>reticulate.conda_binary <span class="operator">=</span> <span class="string">&quot;/opt/conda/bin/conda&quot;</span><span class="punctuation">,</span> SCP_env_name <span class="operator">=</span> <span class="string">&quot;python-scp&quot;</span><span class="punctuation">)</span></span><br><span class="line">SCP<span class="operator">::</span>PrepareEnv<span class="punctuation">(</span></span><br><span class="line">  miniconda_repo <span class="operator">=</span> <span class="string">&quot;https://mirrors.bfsu.edu.cn/anaconda/miniconda&quot;</span><span class="punctuation">,</span></span><br><span class="line">  pip_options <span class="operator">=</span> <span class="string">&quot;-i https://pypi.tuna.tsinghua.edu.cn/simple&quot;</span></span><br><span class="line"><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="准备数据">准备数据</h2>
<ul>
<li><a href="/er-dai-ce-xu-shu-ju-chu-li-zhi-shu-ju-ge-shi-shuo-ming">二代测序数据格式</a></li>
<li><a href="/cellranger-ding-liang--One-Library--Multiple-Flowcells">cellranger 定量</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></pre></td><td class="code"><pre><span class="line">wget https://cf.10xgenomics.com/samples/cell/pbmc3k/pbmc3k_filtered_gene_bc_matrices.tar.gz</span><br><span class="line">tar -zxvf pbmc3k_filtered_gene_bc_matrices.tar.gz</span><br></pre></td></tr></table></figure>
<h2 id="读入数据">读入数据</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><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">pbmc <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>Read10X<span class="punctuation">(</span><span class="string">&#x27;~/data/filtered_gene_bc_matrices/hg19/&#x27;</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>CreateSeuratObject<span class="punctuation">(</span>pbmc<span class="punctuation">,</span> project <span class="operator">=</span> <span class="string">&#x27;pbmc3k&#x27;</span><span class="punctuation">,</span></span><br><span class="line">                            min.cells <span class="operator">=</span> <span class="number">3</span><span class="punctuation">,</span> min.features <span class="operator">=</span> <span class="number">200</span><span class="punctuation">)</span></span><br><span class="line"><span class="comment"># rm(pbmc);gc()</span></span><br><span class="line"><span class="comment"># 线粒体基因</span></span><br><span class="line">sce<span class="punctuation">[[</span><span class="string">&quot;percent.mt&quot;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>PercentageFeatureSet<span class="punctuation">(</span>sce<span class="punctuation">,</span> pattern <span class="operator">=</span> <span class="string">&quot;^MT-&quot;</span><span class="punctuation">)</span></span><br><span class="line"><span class="comment"># 核糖体基因</span></span><br><span class="line">sce<span class="punctuation">[[</span><span class="string">&quot;percent.ribo&quot;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>PercentageFeatureSet<span class="punctuation">(</span>sce<span class="punctuation">,</span> pattern <span class="operator">=</span> <span class="string">&quot;^RP(S|L)&quot;</span><span class="punctuation">)</span></span><br><span class="line"><span class="comment"># 血红蛋白基因 以 &quot;HB&quot; 开头，并且后面紧跟的字符不是 &quot;P&quot; </span></span><br><span class="line">sce<span class="punctuation">[[</span><span class="string">&quot;percent.hb&quot;</span><span class="punctuation">]</span><span class="punctuation">]</span> <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>PercentageFeatureSet<span class="punctuation">(</span>sce<span class="punctuation">,</span> pattern <span class="operator">=</span> <span class="string">&quot;^HB[^(P)]&quot;</span><span class="punctuation">)</span></span><br><span class="line">sce<span class="operator">@</span>meta.data</span><br></pre></td></tr></table></figure>
<h2 id="环境-RNA-校正">环境 RNA 校正</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">decontX_results <span class="operator">&lt;-</span> decontX<span class="operator">::</span>decontX<span class="punctuation">(</span>sce<span class="operator">@</span>assays<span class="operator">$</span>RNA<span class="operator">@</span>counts<span class="punctuation">)</span> </span><br><span class="line">sce<span class="operator">$</span>Contamination <span class="operator">=</span> decontX_results<span class="operator">$</span>contamination</span><br><span class="line">sce<span class="operator">@</span>meta.data</span><br></pre></td></tr></table></figure>
<h2 id="计算细胞周期评分">计算细胞周期评分</h2>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br></pre></td><td class="code"><pre><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>NormalizeData<span class="punctuation">(</span>sce<span class="punctuation">)</span></span><br><span class="line">g2m_genes <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>CaseMatch<span class="punctuation">(</span>search<span class="operator">=</span>Seurat<span class="operator">::</span>cc.genes<span class="operator">$</span>g2m.genes<span class="punctuation">,</span> </span><br><span class="line">                               match<span class="operator">=</span>rownames<span class="punctuation">(</span>sce<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">s_genes <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>CaseMatch<span class="punctuation">(</span>search<span class="operator">=</span>Seurat<span class="operator">::</span>cc.genes<span class="operator">$</span>s.genes<span class="punctuation">,</span> </span><br><span class="line">                             match<span class="operator">=</span>rownames<span class="punctuation">(</span>sce<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>CellCycleScoring<span class="punctuation">(</span>sce<span class="punctuation">,</span> g2m.features<span class="operator">=</span>g2m_genes<span class="punctuation">,</span> s.features<span class="operator">=</span>s_genes<span class="punctuation">)</span></span><br><span class="line">sce<span class="operator">$</span>CC.Difference <span class="operator">&lt;-</span> sce<span class="operator">$</span>S.Score <span class="operator">-</span> sce<span class="operator">$</span>G2M.Score</span><br></pre></td></tr></table></figure>
<h2 id="双细胞过滤">双细胞过滤</h2>
<ul>
<li><a href="/shi-yong-SCTransform-biao-zhun-hua">更多细节</a></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></pre></td><td class="code"><pre><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>SCTransform<span class="punctuation">(</span>sce<span class="punctuation">,</span> vst.flavor <span class="operator">=</span> <span class="string">&quot;v2&quot;</span><span class="punctuation">,</span></span><br><span class="line">                           vars.to.regress <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;percent.mt&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.ribo&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.hb&quot;</span><span class="punctuation">,</span> <span class="string">&quot;Contamination&quot;</span><span class="punctuation">,</span> <span class="string">&quot;CC.Difference&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                           verbose <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span></span><br></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></pre></td><td class="code"><pre><span class="line">sweep.res <span class="operator">&lt;-</span> DoubletFinder<span class="operator">::</span>paramSweep_v3<span class="punctuation">(</span>sce<span class="punctuation">,</span> PCs <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">10</span><span class="punctuation">,</span> sct <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">,</span> num.cores<span class="operator">=</span><span class="number">8</span><span class="punctuation">)</span></span><br><span class="line">sweep.stats <span class="operator">&lt;-</span> DoubletFinder<span class="operator">::</span>summarizeSweep<span class="punctuation">(</span>sweep.res<span class="punctuation">,</span> GT <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">bcmvn <span class="operator">&lt;-</span> DoubletFinder<span class="operator">::</span>find.pK<span class="punctuation">(</span>sweep.stats<span class="punctuation">)</span></span><br></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></pre></td><td class="code"><pre><span class="line"><span class="comment">## Assuming 1.6% doublet formation rate - tailor for your dataset</span></span><br><span class="line">nExp_poi <span class="operator">&lt;-</span> <span class="built_in">round</span><span class="punctuation">(</span><span class="number">0.016</span><span class="operator">*</span>nrow<span class="punctuation">(</span>sce<span class="operator">@</span>meta.data<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">pK_bcmvn <span class="operator">&lt;-</span> <span class="built_in">as.numeric</span><span class="punctuation">(</span><span class="built_in">as.character</span><span class="punctuation">(</span>bcmvn<span class="operator">$</span>pK<span class="punctuation">[</span>which.max<span class="punctuation">(</span>bcmvn<span class="operator">$</span>BCmetric<span class="punctuation">)</span><span class="punctuation">]</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> DoubletFinder<span class="operator">::</span>doubletFinder_v3<span class="punctuation">(</span>sce<span class="punctuation">,</span> PCs <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">10</span><span class="punctuation">,</span> </span><br><span class="line">                                       pN <span class="operator">=</span> <span class="number">0.25</span><span class="punctuation">,</span> pK <span class="operator">=</span> pK_bcmvn<span class="punctuation">,</span> </span><br><span class="line">                                       nExp <span class="operator">=</span> nExp_poi<span class="punctuation">,</span> reuse.pANN <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">,</span> </span><br><span class="line">                                       sct <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">)</span></span><br><span class="line">sce<span class="operator">@</span>meta.data</span><br></pre></td></tr></table></figure>
<h2 id="可视化">可视化</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><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></pre></td><td class="code"><pre><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>RunPCA<span class="punctuation">(</span>sce<span class="punctuation">,</span> assay<span class="operator">=</span><span class="string">&quot;SCT&quot;</span><span class="punctuation">,</span> verbose <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">Seurat<span class="operator">::</span>ElbowPlot<span class="punctuation">(</span>sce<span class="punctuation">,</span> ndims <span class="operator">=</span> <span class="number">50</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>RunUMAP<span class="punctuation">(</span>sce<span class="punctuation">,</span> reduction <span class="operator">=</span> <span class="string">&quot;pca&quot;</span><span class="punctuation">,</span> </span><br><span class="line">                       dims <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">30</span><span class="punctuation">,</span> verbose <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>FindNeighbors<span class="punctuation">(</span>sce<span class="punctuation">,</span> reduction <span class="operator">=</span> <span class="string">&quot;pca&quot;</span><span class="punctuation">,</span> </span><br><span class="line">                             dims <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">30</span><span class="punctuation">,</span> verbose <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">options<span class="punctuation">(</span>repr.plot.width <span class="operator">=</span> <span class="number">8</span><span class="punctuation">,</span> repr.plot.height <span class="operator">=</span> <span class="number">12</span><span class="punctuation">)</span></span><br><span class="line">FeaturePlot<span class="punctuation">(</span>sce<span class="punctuation">,</span> </span><br><span class="line">            features <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;percent.mt&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.ribo&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.hb&quot;</span><span class="punctuation">,</span> <span class="string">&quot;Contamination&quot;</span><span class="punctuation">,</span> <span class="string">&quot;CC.Difference&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span> </span><br><span class="line">            raster<span class="operator">=</span><span class="literal">FALSE</span>       <span class="comment"># 细胞过多时候需要加这个参数</span></span><br><span class="line">           <span class="punctuation">)</span></span><br><span class="line">options<span class="punctuation">(</span>repr.plot.width <span class="operator">=</span> <span class="number">6</span><span class="punctuation">,</span> repr.plot.height <span class="operator">=</span> <span class="number">6</span><span class="punctuation">)</span></span><br><span class="line">DimPlot<span class="punctuation">(</span>sce<span class="punctuation">,</span> reduction <span class="operator">=</span> <span class="string">&quot;umap&quot;</span><span class="punctuation">,</span> group.by <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;DF.classifications_0.25_0.05_43&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">options<span class="punctuation">(</span>repr.plot.width <span class="operator">=</span> <span class="number">12</span><span class="punctuation">,</span> repr.plot.height <span class="operator">=</span> <span class="number">6</span><span class="punctuation">)</span></span><br><span class="line">Seurat<span class="operator">::</span>VlnPlot<span class="punctuation">(</span>sce<span class="punctuation">,</span> features <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;nFeature_RNA&quot;</span><span class="punctuation">,</span> <span class="string">&quot;nCount_RNA&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.mt&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span> ncol <span class="operator">=</span> <span class="number">3</span><span class="punctuation">)</span></span><br><span class="line">plot1 <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>FeatureScatter<span class="punctuation">(</span>sce<span class="punctuation">,</span> feature1 <span class="operator">=</span> <span class="string">&quot;nCount_RNA&quot;</span><span class="punctuation">,</span> feature2 <span class="operator">=</span> <span class="string">&quot;percent.mt&quot;</span><span class="punctuation">)</span></span><br><span class="line">plot2 <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>FeatureScatter<span class="punctuation">(</span>sce<span class="punctuation">,</span> feature1 <span class="operator">=</span> <span class="string">&quot;nCount_RNA&quot;</span><span class="punctuation">,</span> feature2 <span class="operator">=</span> <span class="string">&quot;nFeature_RNA&quot;</span><span class="punctuation">)</span></span><br><span class="line">plot1 <span class="operator">+</span> plot2</span><br></pre></td></tr></table></figure>
<h2 id="过滤低质量细胞">过滤低质量细胞</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">sce <span class="operator">&lt;-</span> subset<span class="punctuation">(</span>sce<span class="punctuation">,</span> DF.classifications_0.25_0.04_43 <span class="operator">!=</span> <span class="string">&#x27;Doublet&#x27;</span></span><br><span class="line">              <span class="operator">&amp;</span> Contamination <span class="operator">&lt;</span> <span class="number">0.2</span></span><br><span class="line"><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="查看分群走向">查看分群走向</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">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>SCTransform<span class="punctuation">(</span>sce<span class="punctuation">,</span> vst.flavor <span class="operator">=</span> <span class="string">&quot;v2&quot;</span><span class="punctuation">,</span></span><br><span class="line">                           vars.to.regress <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;percent.mt&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.ribo&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.hb&quot;</span><span class="punctuation">,</span> <span class="string">&quot;Contamination&quot;</span><span class="punctuation">,</span> <span class="string">&quot;CC.Difference&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                           verbose <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>RunPCA<span class="punctuation">(</span>sce<span class="punctuation">,</span> assay<span class="operator">=</span><span class="string">&quot;SCT&quot;</span><span class="punctuation">,</span> verbose <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">Seurat<span class="operator">::</span>ElbowPlot<span class="punctuation">(</span>sce<span class="punctuation">,</span> ndims <span class="operator">=</span> <span class="number">50</span><span class="punctuation">)</span></span><br></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></pre></td><td class="code"><pre><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>RunUMAP<span class="punctuation">(</span>sce<span class="punctuation">,</span> reduction <span class="operator">=</span> <span class="string">&quot;pca&quot;</span><span class="punctuation">,</span> </span><br><span class="line">                       dims <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">12</span><span class="punctuation">,</span> verbose <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>FindNeighbors<span class="punctuation">(</span>sce<span class="punctuation">,</span> reduction <span class="operator">=</span> <span class="string">&quot;pca&quot;</span><span class="punctuation">,</span> </span><br><span class="line">                             dims <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">12</span><span class="punctuation">,</span> verbose <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br></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></pre></td><td class="code"><pre><span class="line">sce <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>FindClusters<span class="punctuation">(</span></span><br><span class="line">    object <span class="operator">=</span> sce<span class="punctuation">,</span></span><br><span class="line">    resolution <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span>seq<span class="punctuation">(</span><span class="number">.1</span><span class="punctuation">,</span><span class="number">1.6</span><span class="punctuation">,</span><span class="number">.2</span><span class="punctuation">)</span><span class="punctuation">)</span> <span class="comment">#起始粒度，结束粒度，间隔</span></span><br><span class="line"><span class="punctuation">)</span></span><br><span class="line">options<span class="punctuation">(</span>repr.plot.width <span class="operator">=</span> <span class="number">12</span><span class="punctuation">,</span> repr.plot.height <span class="operator">=</span> <span class="number">12</span><span class="punctuation">)</span></span><br><span class="line">require<span class="punctuation">(</span>clustree<span class="punctuation">)</span></span><br><span class="line">clustree<span class="operator">::</span>clustree<span class="punctuation">(</span>sce<span class="operator">@</span>meta.data<span class="punctuation">,</span> prefix <span class="operator">=</span> <span class="string">&quot;SCT_snn_res.&quot;</span><span class="punctuation">)</span></span><br></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></pre></td><td class="code"><pre><span class="line">options<span class="punctuation">(</span>repr.plot.width <span class="operator">=</span> <span class="number">6</span><span class="punctuation">,</span> repr.plot.height <span class="operator">=</span> <span class="number">6</span><span class="punctuation">)</span></span><br><span class="line">DimPlot<span class="punctuation">(</span>sce<span class="punctuation">,</span> reduction <span class="operator">=</span> <span class="string">&quot;umap&quot;</span><span class="punctuation">,</span> group.by <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;SCT_snn_res.0.9&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br></pre></td></tr></table></figure>
<h2 id="可视化-2">可视化</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><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></pre></td><td class="code"><pre><span class="line">sub_celltype <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;0&quot;</span><span class="punctuation">,</span><span class="string">&quot;1&quot;</span> <span class="punctuation">,</span><span class="string">&quot;2&quot;</span> <span class="punctuation">,</span><span class="string">&quot;3&quot;</span><span class="punctuation">)</span></span><br><span class="line">sub.celltype_list <span class="operator">&lt;-</span> sapply<span class="punctuation">(</span>sub_celltype<span class="punctuation">,</span><span class="keyword">function</span><span class="punctuation">(</span>slide<span class="punctuation">)</span><span class="punctuation">&#123;</span></span><br><span class="line">  print<span class="punctuation">(</span>slide<span class="punctuation">)</span></span><br><span class="line">  sub.celltype <span class="operator">&lt;-</span> subset<span class="punctuation">(</span>sce <span class="punctuation">,</span> `SCT_snn_res.0.1` <span class="operator">==</span> slide <span class="punctuation">)</span></span><br><span class="line">  sub.celltype <span class="operator">&lt;-</span> Seurat<span class="operator">::</span>SCTransform<span class="punctuation">(</span>sub.celltype<span class="punctuation">,</span> vst.flavor <span class="operator">=</span> <span class="string">&quot;v2&quot;</span><span class="punctuation">,</span></span><br><span class="line">                           vars.to.regress <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;percent.mt&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.ribo&quot;</span><span class="punctuation">,</span> <span class="string">&quot;percent.hb&quot;</span><span class="punctuation">,</span> <span class="string">&quot;Contamination&quot;</span><span class="punctuation">,</span> <span class="string">&quot;CC.Difference&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                           verbose <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span></span><br><span class="line">  sub.celltype <span class="operator">&lt;-</span> RunPCA<span class="punctuation">(</span>sub.celltype<span class="punctuation">,</span> npcs <span class="operator">=</span> <span class="number">20</span><span class="punctuation">)</span></span><br><span class="line">  sub.celltype <span class="operator">&lt;-</span> FindNeighbors<span class="punctuation">(</span>sub.celltype<span class="punctuation">,</span> dims <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">20</span><span class="punctuation">)</span></span><br><span class="line">  sub.celltype <span class="operator">&lt;-</span> FindClusters<span class="punctuation">(</span>sub.celltype<span class="punctuation">,</span> resolution <span class="operator">=</span> <span class="number">0.9</span><span class="punctuation">)</span></span><br><span class="line">  sub.celltype <span class="operator">&lt;-</span> RunUMAP<span class="punctuation">(</span>sub.celltype<span class="punctuation">,</span> dims <span class="operator">=</span> <span class="number">1</span><span class="operator">:</span><span class="number">20</span><span class="punctuation">)</span></span><br><span class="line">  <span class="built_in">return</span><span class="punctuation">(</span>sub.celltype<span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span><span class="punctuation">)</span> </span><br><span class="line">sub.celltype_list</span><br></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><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br></pre></td><td class="code"><pre><span class="line">require<span class="punctuation">(</span>tidyverse<span class="punctuation">)</span></span><br><span class="line">require<span class="punctuation">(</span>plot1cell<span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">my36colors <span class="operator">&lt;-</span><span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;#E5D2DD&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#53A85F&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#F1BB72&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#F3B1A0&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#D6E7A3&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#57C3F3&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#476D87&#x27;</span><span class="punctuation">,</span></span><br><span class="line">               <span class="string">&#x27;#E95C59&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#E59CC4&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#AB3282&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#23452F&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#BD956A&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#8C549C&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#585658&#x27;</span><span class="punctuation">,</span></span><br><span class="line">               <span class="string">&#x27;#9FA3A8&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#E0D4CA&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#5F3D69&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#C5DEBA&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#58A4C3&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#E4C755&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#F7F398&#x27;</span><span class="punctuation">,</span></span><br><span class="line">               <span class="string">&#x27;#AA9A59&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#E63863&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#E39A35&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#C1E6F3&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#6778AE&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#91D0BE&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#B53E2B&#x27;</span><span class="punctuation">,</span></span><br><span class="line">               <span class="string">&#x27;#712820&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#DCC1DD&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#CCE0F5&#x27;</span><span class="punctuation">,</span>  <span class="string">&#x27;#CCC9E6&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#625D9E&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#68A180&#x27;</span><span class="punctuation">,</span> <span class="string">&#x27;#3A6963&#x27;</span><span class="punctuation">,</span></span><br><span class="line">               <span class="string">&#x27;#968175&#x27;</span></span><br><span class="line"><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">plot_circlize_change <span class="operator">&lt;-</span> <span class="keyword">function</span> <span class="punctuation">(</span>data_plot<span class="punctuation">,</span> do.label <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">,</span> contour.levels <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="number">0.2</span><span class="punctuation">,</span> <span class="number">0.3</span><span class="punctuation">)</span><span class="punctuation">,</span> </span><br><span class="line">          pt.size <span class="operator">=</span> <span class="number">0.5</span><span class="punctuation">,</span> kde2d.n <span class="operator">=</span> <span class="number">1000</span><span class="punctuation">,</span> contour.nlevels <span class="operator">=</span> <span class="number">100</span><span class="punctuation">,</span> bg.color <span class="operator">=</span> <span class="string">&quot;#F9F2E4&quot;</span><span class="punctuation">,</span> </span><br><span class="line">          col.use <span class="operator">=</span> <span class="literal">NULL</span><span class="punctuation">,</span> label.cex <span class="operator">=</span> <span class="number">0.5</span><span class="punctuation">,</span> labels.cex <span class="operator">=</span> <span class="number">0.5</span><span class="punctuation">,</span> circos.cex <span class="operator">=</span> <span class="number">0.5</span> <span class="punctuation">,</span>repel <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span> </span><br><span class="line"><span class="punctuation">&#123;</span></span><br><span class="line">  centers <span class="operator">&lt;-</span> data_plot <span class="operator">%&gt;%</span> dplyr<span class="operator">::</span>group_by<span class="punctuation">(</span>Cluster<span class="punctuation">)</span> <span class="operator">%&gt;%</span> summarise<span class="punctuation">(</span>x <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> x<span class="punctuation">)</span><span class="punctuation">,</span> </span><br><span class="line">                                                                  y <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> y<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">  z <span class="operator">&lt;-</span> MASS<span class="operator">::</span>kde2d<span class="punctuation">(</span>data_plot<span class="operator">$</span>x<span class="punctuation">,</span> data_plot<span class="operator">$</span>y<span class="punctuation">,</span> n <span class="operator">=</span> kde2d.n<span class="punctuation">)</span></span><br><span class="line">  celltypes <span class="operator">&lt;-</span> <span class="built_in">names</span><span class="punctuation">(</span>table<span class="punctuation">(</span>data_plot<span class="operator">$</span>Cluster<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">  cell_colors <span class="operator">&lt;-</span> <span class="punctuation">(</span>scales<span class="operator">::</span>hue_pal<span class="punctuation">(</span><span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span>celltypes<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">  <span class="keyword">if</span> <span class="punctuation">(</span><span class="operator">!</span><span class="built_in">is.null</span><span class="punctuation">(</span>col.use<span class="punctuation">)</span><span class="punctuation">)</span> <span class="punctuation">&#123;</span></span><br><span class="line">    cell_colors <span class="operator">=</span> col.use</span><br><span class="line">    col_df <span class="operator">&lt;-</span> data.frame<span class="punctuation">(</span>Cluster <span class="operator">=</span> celltypes<span class="punctuation">,</span> color2 <span class="operator">=</span> col.use<span class="punctuation">)</span></span><br><span class="line">    cells_order <span class="operator">&lt;-</span> rownames<span class="punctuation">(</span>data_plot<span class="punctuation">)</span></span><br><span class="line">    data_plot <span class="operator">&lt;-</span> merge<span class="punctuation">(</span>data_plot<span class="punctuation">,</span> col_df<span class="punctuation">,</span> by <span class="operator">=</span> <span class="string">&quot;Cluster&quot;</span><span class="punctuation">)</span></span><br><span class="line">    rownames<span class="punctuation">(</span>data_plot<span class="punctuation">)</span> <span class="operator">&lt;-</span> data_plot<span class="operator">$</span>cells</span><br><span class="line">    data_plot <span class="operator">&lt;-</span> data_plot<span class="punctuation">[</span>cells_order<span class="punctuation">,</span> <span class="punctuation">]</span></span><br><span class="line">    data_plot<span class="operator">$</span>Colors <span class="operator">&lt;-</span> data_plot<span class="operator">$</span>color2</span><br><span class="line">  <span class="punctuation">&#125;</span></span><br><span class="line">  circos.clear<span class="punctuation">(</span><span class="punctuation">)</span></span><br><span class="line">  par<span class="punctuation">(</span>bg <span class="operator">=</span> bg.color<span class="punctuation">)</span></span><br><span class="line">  circos.par<span class="punctuation">(</span>cell.padding <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="number">0</span><span class="punctuation">,</span> <span class="number">0</span><span class="punctuation">,</span> <span class="number">0</span><span class="punctuation">,</span> <span class="number">0</span><span class="punctuation">)</span><span class="punctuation">,</span> track.margin <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="number">0.01</span><span class="punctuation">,</span> </span><br><span class="line">                                                            <span class="number">0</span><span class="punctuation">)</span><span class="punctuation">,</span> track.height <span class="operator">=</span> <span class="number">0.01</span><span class="punctuation">,</span> gap.degree <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="built_in">rep</span><span class="punctuation">(</span><span class="number">2</span><span class="punctuation">,</span> <span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span>celltypes<span class="punctuation">)</span> <span class="operator">-</span> </span><br><span class="line">                                                                                                              <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">,</span> <span class="number">12</span><span class="punctuation">)</span><span class="punctuation">,</span> points.overflow.warning <span class="operator">=</span> <span class="literal">FALSE</span><span class="punctuation">)</span></span><br><span class="line">  circos.initialize<span class="punctuation">(</span>sectors <span class="operator">=</span> data_plot<span class="operator">$</span>Cluster<span class="punctuation">,</span> x <span class="operator">=</span> data_plot<span class="operator">$</span>x_polar2<span class="punctuation">)</span></span><br><span class="line">  circos.track<span class="punctuation">(</span>data_plot<span class="operator">$</span>Cluster<span class="punctuation">,</span> data_plot<span class="operator">$</span>x_polar2<span class="punctuation">,</span> y <span class="operator">=</span> data_plot<span class="operator">$</span>dim2<span class="punctuation">,</span> </span><br><span class="line">               bg.border <span class="operator">=</span> <span class="literal">NA</span><span class="punctuation">,</span> panel.fun <span class="operator">=</span> <span class="keyword">function</span><span class="punctuation">(</span>x<span class="punctuation">,</span> y<span class="punctuation">)</span> <span class="punctuation">&#123;</span></span><br><span class="line">                 circos.text<span class="punctuation">(</span>CELL_META<span class="operator">$</span>xcenter<span class="punctuation">,</span> CELL_META<span class="operator">$</span>cell.ylim<span class="punctuation">[</span><span class="number">2</span><span class="punctuation">]</span> <span class="operator">+</span> </span><br><span class="line">                               mm_y<span class="punctuation">(</span><span class="number">4</span><span class="punctuation">)</span><span class="punctuation">,</span> CELL_META<span class="operator">$</span>sector.index<span class="punctuation">,</span> cex <span class="operator">=</span> labels.cex<span class="punctuation">,</span></span><br><span class="line">                             col <span class="operator">=</span> <span class="string">&quot;black&quot;</span><span class="punctuation">,</span> facing <span class="operator">=</span> <span class="string">&quot;bending.inside&quot;</span><span class="punctuation">,</span> niceFacing <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">)</span></span><br><span class="line">                 <span class="comment">#circos.axis(labels.cex = 0.3, col = &quot;black&quot;, labels.col = &quot;black&quot;)</span></span><br><span class="line">                 circos.axis<span class="punctuation">(</span>labels.cex <span class="operator">=</span> circos.cex<span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&quot;black&quot;</span><span class="punctuation">,</span> labels.col <span class="operator">=</span> <span class="string">&quot;black&quot;</span><span class="punctuation">)</span></span><br><span class="line">               <span class="punctuation">&#125;</span><span class="punctuation">)</span></span><br><span class="line">  <span class="keyword">for</span> <span class="punctuation">(</span>i <span class="keyword">in</span> <span class="number">1</span><span class="operator">:</span><span class="built_in">length</span><span class="punctuation">(</span>celltypes<span class="punctuation">)</span><span class="punctuation">)</span> <span class="punctuation">&#123;</span></span><br><span class="line">    dd <span class="operator">&lt;-</span> data_plot<span class="punctuation">[</span>data_plot<span class="operator">$</span>Cluster <span class="operator">==</span> celltypes<span class="punctuation">[</span>i<span class="punctuation">]</span><span class="punctuation">,</span> <span class="punctuation">]</span></span><br><span class="line">    circos.segments<span class="punctuation">(</span>x0 <span class="operator">=</span> <span class="built_in">min</span><span class="punctuation">(</span>dd<span class="operator">$</span>x_polar2<span class="punctuation">)</span><span class="punctuation">,</span> y0 <span class="operator">=</span> <span class="number">0</span><span class="punctuation">,</span> x1 <span class="operator">=</span> <span class="built_in">max</span><span class="punctuation">(</span>dd<span class="operator">$</span>x_polar2<span class="punctuation">)</span><span class="punctuation">,</span> </span><br><span class="line">                    y1 <span class="operator">=</span> <span class="number">0</span><span class="punctuation">,</span> col <span class="operator">=</span> cell_colors<span class="punctuation">[</span>i<span class="punctuation">]</span><span class="punctuation">,</span> lwd <span class="operator">=</span> <span class="number">3</span><span class="punctuation">,</span> sector.index <span class="operator">=</span> celltypes<span class="punctuation">[</span>i<span class="punctuation">]</span><span class="punctuation">)</span></span><br><span class="line">  <span class="punctuation">&#125;</span></span><br><span class="line">  text<span class="punctuation">(</span>x <span class="operator">=</span> <span class="number">1</span><span class="punctuation">,</span> y <span class="operator">=</span> <span class="number">0.1</span><span class="punctuation">,</span> labels <span class="operator">=</span> <span class="string">&quot;Cluster&quot;</span><span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.4</span><span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&quot;black&quot;</span><span class="punctuation">,</span> </span><br><span class="line">       srt <span class="operator">=</span> <span class="operator">-</span><span class="number">90</span><span class="punctuation">)</span></span><br><span class="line">  points<span class="punctuation">(</span>data_plot<span class="operator">$</span>x<span class="punctuation">,</span> data_plot<span class="operator">$</span>y<span class="punctuation">,</span> pch <span class="operator">=</span> <span class="number">19</span><span class="punctuation">,</span> col <span class="operator">=</span> alpha<span class="punctuation">(</span>data_plot<span class="operator">$</span>Colors<span class="punctuation">,</span> </span><br><span class="line">                                                         <span class="number">0.9</span><span class="punctuation">)</span><span class="punctuation">,</span> cex <span class="operator">=</span> pt.size<span class="punctuation">)</span></span><br><span class="line">  contour<span class="punctuation">(</span>z<span class="punctuation">,</span> drawlabels <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">,</span> nlevels <span class="operator">=</span> <span class="number">100</span><span class="punctuation">,</span> levels <span class="operator">=</span> contour.levels<span class="punctuation">,</span> </span><br><span class="line">          col <span class="operator">=</span> <span class="string">&quot;#ae9c76&quot;</span><span class="punctuation">,</span> add <span class="operator">=</span> <span class="literal">TRUE</span><span class="punctuation">)</span></span><br><span class="line">  <span class="keyword">if</span> <span class="punctuation">(</span>do.label<span class="punctuation">)</span> <span class="punctuation">&#123;</span></span><br><span class="line">    <span class="keyword">if</span> <span class="punctuation">(</span>repel<span class="punctuation">)</span> <span class="punctuation">&#123;</span></span><br><span class="line">      textplot<span class="punctuation">(</span>x <span class="operator">=</span> centers<span class="operator">$</span>x<span class="punctuation">,</span> y <span class="operator">=</span> centers<span class="operator">$</span>y<span class="punctuation">,</span> words <span class="operator">=</span> centers<span class="operator">$</span>Cluster<span class="punctuation">,</span> </span><br><span class="line">               cex <span class="operator">=</span> label.cex<span class="punctuation">,</span> new <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">,</span> show.lines <span class="operator">=</span> <span class="built_in">F</span><span class="punctuation">)</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line">    <span class="keyword">else</span> <span class="punctuation">&#123;</span></span><br><span class="line">      text<span class="punctuation">(</span>centers<span class="operator">$</span>x<span class="punctuation">,</span> centers<span class="operator">$</span>y<span class="punctuation">,</span> labels <span class="operator">=</span> centers<span class="operator">$</span>Cluster<span class="punctuation">,</span> </span><br><span class="line">           cex <span class="operator">=</span> label.cex<span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&quot;black&quot;</span><span class="punctuation">)</span></span><br><span class="line">    <span class="punctuation">&#125;</span></span><br><span class="line">  <span class="punctuation">&#125;</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br></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><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br><span class="line">58</span><br><span class="line">59</span><br><span class="line">60</span><br><span class="line">61</span><br><span class="line">62</span><br><span class="line">63</span><br><span class="line">64</span><br><span class="line">65</span><br><span class="line">66</span><br><span class="line">67</span><br><span class="line">68</span><br><span class="line">69</span><br><span class="line">70</span><br><span class="line">71</span><br><span class="line">72</span><br><span class="line">73</span><br><span class="line">74</span><br><span class="line">75</span><br><span class="line">76</span><br><span class="line">77</span><br><span class="line">78</span><br><span class="line">79</span><br><span class="line">80</span><br><span class="line">81</span><br><span class="line">82</span><br><span class="line">83</span><br><span class="line">84</span><br><span class="line">85</span><br><span class="line">86</span><br><span class="line">87</span><br><span class="line">88</span><br><span class="line">89</span><br><span class="line">90</span><br><span class="line">91</span><br><span class="line">92</span><br><span class="line">93</span><br><span class="line">94</span><br><span class="line">95</span><br><span class="line">96</span><br><span class="line">97</span><br><span class="line">98</span><br><span class="line">99</span><br><span class="line">100</span><br><span class="line">101</span><br><span class="line">102</span><br><span class="line">103</span><br><span class="line">104</span><br><span class="line">105</span><br><span class="line">106</span><br><span class="line">107</span><br><span class="line">108</span><br><span class="line">109</span><br><span class="line">110</span><br><span class="line">111</span><br><span class="line">112</span><br><span class="line">113</span><br><span class="line">114</span><br><span class="line">115</span><br><span class="line">116</span><br><span class="line">117</span><br><span class="line">118</span><br><span class="line">119</span><br></pre></td><td class="code"><pre><span class="line"><span class="comment">###Prepare data for ploting 准备圈图数据</span></span><br><span class="line">circ_data <span class="operator">&lt;-</span> plot1cell<span class="operator">::</span>prepare_circlize_data<span class="punctuation">(</span>sce<span class="punctuation">,</span> scale <span class="operator">=</span> <span class="number">0.7</span><span class="punctuation">)</span> <span class="comment"># 画出框了就调小 scale</span></span><br><span class="line">set.seed<span class="punctuation">(</span><span class="number">1234</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 设置细胞分群信息的颜色</span></span><br><span class="line">cluster_colors <span class="operator">&lt;-</span> circlize<span class="operator">::</span>rand_color<span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span>levels<span class="punctuation">(</span>sce<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">group_colors <span class="operator">&lt;-</span> circlize<span class="operator">::</span>rand_color<span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span><span class="built_in">names</span><span class="punctuation">(</span>table<span class="punctuation">(</span>sce<span class="operator">$</span>`SCT_snn_res.0.1`<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">rep_colors <span class="operator">&lt;-</span> circlize<span class="operator">::</span>rand_color<span class="punctuation">(</span><span class="built_in">length</span><span class="punctuation">(</span><span class="built_in">names</span><span class="punctuation">(</span>table<span class="punctuation">(</span>sce<span class="operator">$</span>orig.ident<span class="punctuation">)</span><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"># 绘制细胞分群圈图</span></span><br><span class="line"><span class="punctuation">&#123;</span>pdf<span class="punctuation">(</span>file <span class="operator">=</span> <span class="string">&#x27;umap_circlize.plot.pdf&#x27;</span><span class="punctuation">,</span> width <span class="operator">=</span> <span class="number">9</span><span class="punctuation">,</span> height <span class="operator">=</span> <span class="number">6</span><span class="punctuation">)</span> <span class="comment"># 导出PDF开始</span></span><br><span class="line"></span><br><span class="line">options<span class="punctuation">(</span>repr.plot.width <span class="operator">=</span> <span class="number">12</span><span class="punctuation">,</span> repr.plot.height <span class="operator">=</span> <span class="number">8</span><span class="punctuation">)</span></span><br><span class="line">plot_circlize_change<span class="punctuation">(</span>circ_data<span class="punctuation">,</span>do.label <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">,</span> pt.size <span class="operator">=</span> <span class="number">0.01</span><span class="punctuation">,</span> </span><br><span class="line">              col.use <span class="operator">=</span> cluster_colors <span class="punctuation">,</span></span><br><span class="line">              bg.color <span class="operator">=</span> <span class="string">&#x27;#F9F2E5&#x27;</span><span class="punctuation">,</span> </span><br><span class="line">              kde2d.n <span class="operator">=</span> <span class="number">1000</span><span class="punctuation">,</span> </span><br><span class="line">              repel <span class="operator">=</span> <span class="built_in">T</span><span class="punctuation">,</span> </span><br><span class="line">              labels.cex <span class="operator">=</span> <span class="number">1</span><span class="punctuation">,</span> </span><br><span class="line">              circos.cex <span class="operator">=</span> <span class="number">0.5</span><span class="punctuation">,</span></span><br><span class="line">              label.cex <span class="operator">=</span> <span class="number">1</span><span class="punctuation">)</span></span><br><span class="line"> </span><br><span class="line">plot1cell<span class="operator">::</span>add_track<span class="punctuation">(</span>circ_data<span class="punctuation">,</span> </span><br><span class="line">          group <span class="operator">=</span> <span class="string">&quot;SCT_snn_res.0.1&quot;</span><span class="punctuation">,</span> </span><br><span class="line">          colors <span class="operator">=</span> group_colors<span class="punctuation">,</span> track_num <span class="operator">=</span> <span class="number">2</span><span class="punctuation">)</span> <span class="comment">## can change it to one of the columns in the meta data of your seurat object</span></span><br><span class="line">plot1cell<span class="operator">::</span>add_track<span class="punctuation">(</span>circ_data<span class="punctuation">,</span> </span><br><span class="line">          group <span class="operator">=</span> <span class="string">&quot;orig.ident&quot;</span><span class="punctuation">,</span></span><br><span class="line">          colors <span class="operator">=</span> rep_colors<span class="punctuation">,</span> track_num <span class="operator">=</span> <span class="number">3</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 左下</span></span><br><span class="line">sub_index <span class="operator">=</span> <span class="number">1</span></span><br><span class="line">subcolors <span class="operator">&lt;-</span> my36colors<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span>nlevels<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">sub_1_meta<span class="operator">&lt;-</span>get_metadata<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span> color <span class="operator">=</span> subcolors<span class="punctuation">)</span></span><br><span class="line">sub_1_meta <span class="operator">%&gt;%</span></span><br><span class="line">  dplyr<span class="operator">::</span>group_by<span class="punctuation">(</span>seurat_clusters<span class="punctuation">)</span> <span class="operator">%&gt;%</span></span><br><span class="line">  summarize<span class="punctuation">(</span>x <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> x<span class="punctuation">)</span><span class="punctuation">,</span>y <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> y<span class="punctuation">)</span><span class="punctuation">)</span> <span class="operator">-&gt;</span> centers_1</span><br><span class="line"></span><br><span class="line">points<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">1.2</span><span class="punctuation">,</span>sub_1_meta<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">0.73</span><span class="punctuation">,</span> pch <span class="operator">=</span> <span class="number">19</span><span class="punctuation">,</span> col <span class="operator">=</span> alpha<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>Colors<span class="punctuation">,</span><span class="number">0.9</span><span class="punctuation">)</span><span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.1</span><span class="punctuation">)</span>;</span><br><span class="line">text<span class="punctuation">(</span>centers_1<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">1.2</span><span class="punctuation">,</span>centers_1<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">0.73</span><span class="punctuation">,</span> labels<span class="operator">=</span>centers_1<span class="operator">$</span>seurat_clusters<span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.6</span><span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&#x27;black&#x27;</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 右上</span></span><br><span class="line">sub_index <span class="operator">=</span> <span class="number">2</span></span><br><span class="line">subcolors <span class="operator">&lt;-</span> my36colors<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span>nlevels<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">sub_1_meta<span class="operator">&lt;-</span>get_metadata<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span> color <span class="operator">=</span> subcolors<span class="punctuation">)</span></span><br><span class="line">sub_1_meta <span class="operator">%&gt;%</span></span><br><span class="line">  dplyr<span class="operator">::</span>group_by<span class="punctuation">(</span>seurat_clusters<span class="punctuation">)</span> <span class="operator">%&gt;%</span></span><br><span class="line">  summarize<span class="punctuation">(</span>x <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> x<span class="punctuation">)</span><span class="punctuation">,</span>y <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> y<span class="punctuation">)</span><span class="punctuation">)</span> <span class="operator">-&gt;</span> centers_1</span><br><span class="line"></span><br><span class="line">points<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">1.2</span><span class="punctuation">,</span>sub_1_meta<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">0.73</span><span class="punctuation">,</span> pch <span class="operator">=</span> <span class="number">19</span><span class="punctuation">,</span> col <span class="operator">=</span> alpha<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>Colors<span class="punctuation">,</span><span class="number">0.9</span><span class="punctuation">)</span><span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.1</span><span class="punctuation">)</span>;</span><br><span class="line">text<span class="punctuation">(</span>centers_1<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">1.2</span><span class="punctuation">,</span>centers_1<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">0.73</span><span class="punctuation">,</span> labels<span class="operator">=</span>centers_1<span class="operator">$</span>seurat_clusters<span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.6</span><span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&#x27;black&#x27;</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 左上</span></span><br><span class="line">sub_index <span class="operator">=</span> <span class="number">3</span></span><br><span class="line">subcolors <span class="operator">&lt;-</span> my36colors<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span>nlevels<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">sub_1_meta<span class="operator">&lt;-</span>get_metadata<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span> color <span class="operator">=</span> subcolors<span class="punctuation">)</span></span><br><span class="line">sub_1_meta <span class="operator">%&gt;%</span></span><br><span class="line">  dplyr<span class="operator">::</span>group_by<span class="punctuation">(</span>seurat_clusters<span class="punctuation">)</span> <span class="operator">%&gt;%</span></span><br><span class="line">  summarize<span class="punctuation">(</span>x <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> x<span class="punctuation">)</span><span class="punctuation">,</span>y <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> y<span class="punctuation">)</span><span class="punctuation">)</span> <span class="operator">-&gt;</span> centers_1</span><br><span class="line"></span><br><span class="line">points<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">1.2</span><span class="punctuation">,</span>sub_1_meta<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">0.73</span><span class="punctuation">,</span> pch <span class="operator">=</span> <span class="number">19</span><span class="punctuation">,</span> col <span class="operator">=</span> alpha<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>Colors<span class="punctuation">,</span><span class="number">0.9</span><span class="punctuation">)</span><span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.1</span><span class="punctuation">)</span>;</span><br><span class="line">text<span class="punctuation">(</span>centers_1<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">1.2</span><span class="punctuation">,</span>centers_1<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">0.73</span><span class="punctuation">,</span> labels<span class="operator">=</span>centers_1<span class="operator">$</span>seurat_clusters<span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.6</span><span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&#x27;black&#x27;</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 右下</span></span><br><span class="line">sub_index <span class="operator">=</span> <span class="number">4</span></span><br><span class="line">subcolors <span class="operator">&lt;-</span> my36colors<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span>nlevels<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">sub_1_meta<span class="operator">&lt;-</span>get_metadata<span class="punctuation">(</span>sub.celltype_list<span class="punctuation">[[</span>sub_index<span class="punctuation">]</span><span class="punctuation">]</span><span class="punctuation">,</span> color <span class="operator">=</span> subcolors<span class="punctuation">)</span></span><br><span class="line">sub_1_meta <span class="operator">%&gt;%</span></span><br><span class="line">  dplyr<span class="operator">::</span>group_by<span class="punctuation">(</span>seurat_clusters<span class="punctuation">)</span> <span class="operator">%&gt;%</span></span><br><span class="line">  summarize<span class="punctuation">(</span>x <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> x<span class="punctuation">)</span><span class="punctuation">,</span>y <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> y<span class="punctuation">)</span><span class="punctuation">)</span> <span class="operator">-&gt;</span> centers_1</span><br><span class="line"></span><br><span class="line">points<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">1.2</span><span class="punctuation">,</span>sub_1_meta<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">0.73</span><span class="punctuation">,</span> pch <span class="operator">=</span> <span class="number">19</span><span class="punctuation">,</span> col <span class="operator">=</span> alpha<span class="punctuation">(</span>sub_1_meta<span class="operator">$</span>Colors<span class="punctuation">,</span><span class="number">0.9</span><span class="punctuation">)</span><span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.1</span><span class="punctuation">)</span>;</span><br><span class="line">text<span class="punctuation">(</span>centers_1<span class="operator">$</span>x<span class="operator">*</span><span class="number">0.32</span><span class="operator">+</span><span class="number">1.2</span><span class="punctuation">,</span>centers_1<span class="operator">$</span>y<span class="operator">*</span><span class="number">0.32</span><span class="operator">-</span><span class="number">0.73</span><span class="punctuation">,</span> labels<span class="operator">=</span>centers_1<span class="operator">$</span>seurat_clusters<span class="punctuation">,</span> cex <span class="operator">=</span> <span class="number">0.6</span><span class="punctuation">,</span> col <span class="operator">=</span> <span class="string">&#x27;black&#x27;</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"></span><br><span class="line">title_text <span class="operator">&lt;-</span> <span class="keyword">function</span><span class="punctuation">(</span>x0<span class="punctuation">,</span> y0<span class="punctuation">,</span> x1<span class="punctuation">,</span> y1<span class="punctuation">,</span> text<span class="punctuation">,</span> rectArgs <span class="operator">=</span> <span class="literal">NULL</span><span class="punctuation">,</span> textArgs <span class="operator">=</span> <span class="literal">NULL</span><span class="punctuation">)</span> <span class="punctuation">&#123;</span></span><br><span class="line">  center <span class="operator">&lt;-</span> <span class="built_in">c</span><span class="punctuation">(</span>mean<span class="punctuation">(</span><span class="built_in">c</span><span class="punctuation">(</span>x0<span class="punctuation">,</span> x1<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">,</span> mean<span class="punctuation">(</span><span class="built_in">c</span><span class="punctuation">(</span>y0<span class="punctuation">,</span> y1<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">  do.call<span class="punctuation">(</span><span class="string">&#x27;rect&#x27;</span><span class="punctuation">,</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="built_in">list</span><span class="punctuation">(</span>xleft <span class="operator">=</span> x0<span class="punctuation">,</span> ybottom <span class="operator">=</span> y0<span class="punctuation">,</span> xright <span class="operator">=</span> x1<span class="punctuation">,</span> ytop <span class="operator">=</span> y1<span class="punctuation">)</span><span class="punctuation">,</span> rectArgs<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line">  do.call<span class="punctuation">(</span><span class="string">&#x27;text&#x27;</span><span class="punctuation">,</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="built_in">list</span><span class="punctuation">(</span>x <span class="operator">=</span> center<span class="punctuation">[</span><span class="number">1</span><span class="punctuation">]</span><span class="punctuation">,</span> y <span class="operator">=</span> center<span class="punctuation">[</span><span class="number">2</span><span class="punctuation">]</span><span class="punctuation">,</span> labels <span class="operator">=</span> text<span class="punctuation">)</span><span class="punctuation">,</span> textArgs<span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"><span class="punctuation">&#125;</span></span><br><span class="line"></span><br><span class="line"><span class="comment"># 四周的title </span></span><br><span class="line">title_text<span class="punctuation">(</span>x0 <span class="operator">=</span> <span class="operator">-</span><span class="number">1.35</span><span class="punctuation">,</span> x1 <span class="operator">=</span> <span class="operator">-</span><span class="number">1.05</span><span class="punctuation">,</span> y0 <span class="operator">=</span> <span class="operator">-</span><span class="number">1.06</span><span class="punctuation">,</span> y1<span class="operator">=</span><span class="operator">-</span><span class="number">1</span><span class="punctuation">,</span> text <span class="operator">=</span> <span class="string">&#x27;type 1 cells&#x27;</span><span class="punctuation">,</span></span><br><span class="line">           rectArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>border<span class="operator">=</span><span class="string">&#x27;#F9F2E4&#x27;</span><span class="punctuation">,</span>lwd<span class="operator">=</span><span class="number">0.5</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">           textArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>col<span class="operator">=</span><span class="string">&#x27;black&#x27;</span><span class="punctuation">,</span>cex <span class="operator">=</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">title_text<span class="punctuation">(</span>x0 <span class="operator">=</span> <span class="number">1.05</span><span class="punctuation">,</span> x1 <span class="operator">=</span> <span class="number">1.35</span><span class="punctuation">,</span> y0 <span class="operator">=</span> <span class="operator">-</span><span class="number">1.06</span><span class="punctuation">,</span> y1<span class="operator">=</span><span class="operator">-</span><span class="number">1</span><span class="punctuation">,</span> text <span class="operator">=</span> <span class="string">&#x27;type 2 cells&#x27;</span><span class="punctuation">,</span></span><br><span class="line">           rectArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>border<span class="operator">=</span><span class="string">&#x27;#F9F2E4&#x27;</span><span class="punctuation">,</span>lwd<span class="operator">=</span><span class="number">0.5</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">           textArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>col<span class="operator">=</span><span class="string">&#x27;black&#x27;</span><span class="punctuation">,</span>cex <span class="operator">=</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">title_text<span class="punctuation">(</span>x0 <span class="operator">=</span> <span class="operator">-</span><span class="number">1.35</span><span class="punctuation">,</span> x1 <span class="operator">=</span> <span class="operator">-</span><span class="number">1.05</span><span class="punctuation">,</span> y0 <span class="operator">=</span> <span class="number">1.06</span><span class="punctuation">,</span> y1<span class="operator">=</span><span class="number">1</span><span class="punctuation">,</span> text <span class="operator">=</span> <span class="string">&#x27;type 3 cells&#x27;</span><span class="punctuation">,</span></span><br><span class="line">           rectArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>border<span class="operator">=</span><span class="string">&#x27;#F9F2E4&#x27;</span><span class="punctuation">,</span>lwd<span class="operator">=</span><span class="number">0.5</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">           textArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>col<span class="operator">=</span><span class="string">&#x27;black&#x27;</span><span class="punctuation">,</span>cex <span class="operator">=</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">title_text<span class="punctuation">(</span>x0 <span class="operator">=</span> <span class="number">1.05</span><span class="punctuation">,</span> x1 <span class="operator">=</span> <span class="number">1.35</span><span class="punctuation">,</span> y0 <span class="operator">=</span> <span class="number">1.06</span><span class="punctuation">,</span> y1<span class="operator">=</span><span class="number">1</span><span class="punctuation">,</span> text <span class="operator">=</span> <span class="string">&#x27;type 4 cells&#x27;</span><span class="punctuation">,</span></span><br><span class="line">           rectArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>border<span class="operator">=</span><span class="string">&#x27;#F9F2E4&#x27;</span><span class="punctuation">,</span>lwd<span class="operator">=</span><span class="number">0.5</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">           textArgs <span class="operator">=</span> <span class="built_in">list</span><span class="punctuation">(</span>col<span class="operator">=</span><span class="string">&#x27;black&#x27;</span><span class="punctuation">,</span>cex <span class="operator">=</span> <span class="number">1</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line"></span><br><span class="line"><span class="comment">#plot group#</span></span><br><span class="line">Idents<span class="punctuation">(</span>sce<span class="punctuation">)</span> <span class="operator">&lt;-</span> <span class="string">&quot;SCT_snn_res.0.1&quot;</span></span><br><span class="line">col_use <span class="operator">&lt;-</span> my36colors<span class="punctuation">[</span><span class="number">1</span><span class="operator">:</span>nlevels<span class="punctuation">(</span>sce<span class="punctuation">)</span><span class="punctuation">]</span></span><br><span class="line">cc <span class="operator">&lt;-</span> get_metadata<span class="punctuation">(</span>sce<span class="punctuation">,</span> color <span class="operator">=</span> col_use<span class="punctuation">)</span></span><br><span class="line">cc <span class="operator">%&gt;%</span></span><br><span class="line">  dplyr<span class="operator">::</span>group_by<span class="punctuation">(</span><span class="string">&quot;SCT_snn_res.0.1&quot;</span><span class="punctuation">)</span> <span class="operator">%&gt;%</span></span><br><span class="line">  summarize<span class="punctuation">(</span>x <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> x<span class="punctuation">)</span><span class="punctuation">,</span>y <span class="operator">=</span> median<span class="punctuation">(</span>x <span class="operator">=</span> y<span class="punctuation">)</span><span class="punctuation">)</span> <span class="operator">-&gt;</span> centers</span><br><span class="line">col_group <span class="operator">&lt;-</span>  <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&#x27;#bff542&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;#83f78f&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;#EBA1A2&#x27;</span><span class="punctuation">,</span><span class="string">&#x27;#D70016&#x27;</span><span class="punctuation">)</span></span><br><span class="line">lgd_points <span class="operator">=</span> Legend<span class="punctuation">(</span>labels <span class="operator">=</span> <span class="built_in">names</span><span class="punctuation">(</span>table<span class="punctuation">(</span>cc<span class="operator">$</span>`SCT_snn_res.0.1`<span class="punctuation">)</span><span class="punctuation">)</span><span class="punctuation">,</span> type <span class="operator">=</span> <span class="string">&quot;points&quot;</span><span class="punctuation">,</span> </span><br><span class="line">                    title_position <span class="operator">=</span> <span class="string">&quot;topleft&quot;</span><span class="punctuation">,</span> </span><br><span class="line">                    title <span class="operator">=</span> <span class="string">&quot;Group&quot;</span><span class="punctuation">,</span></span><br><span class="line">                    title_gp <span class="operator">=</span> gpar<span class="punctuation">(</span>col<span class="operator">=</span><span class="string">&#x27;black&#x27;</span><span class="punctuation">,</span>fontsize <span class="operator">=</span> <span class="number">7</span><span class="punctuation">,</span> fontface<span class="operator">=</span><span class="string">&#x27;bold&#x27;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                    legend_gp <span class="operator">=</span> gpar<span class="punctuation">(</span>col <span class="operator">=</span> col_group<span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                    labels_gp <span class="operator">=</span> gpar<span class="punctuation">(</span>col<span class="operator">=</span><span class="string">&#x27;black&#x27;</span><span class="punctuation">,</span>fontsize <span class="operator">=</span> <span class="number">5</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                    grid_height <span class="operator">=</span> unit<span class="punctuation">(</span><span class="number">2</span><span class="punctuation">,</span> <span class="string">&quot;mm&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                    grid_width <span class="operator">=</span> unit<span class="punctuation">(</span><span class="number">2</span><span class="punctuation">,</span> <span class="string">&quot;mm&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">                    background <span class="operator">=</span> col_group<span class="punctuation">)</span></span><br><span class="line">draw<span class="punctuation">(</span>lgd_points<span class="punctuation">,</span> x <span class="operator">=</span> unit<span class="punctuation">(</span><span class="number">15</span><span class="punctuation">,</span> <span class="string">&quot;mm&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span> y <span class="operator">=</span> unit<span class="punctuation">(</span><span class="number">50</span><span class="punctuation">,</span> <span class="string">&quot;mm&quot;</span><span class="punctuation">)</span><span class="punctuation">,</span></span><br><span class="line">     just <span class="operator">=</span> <span class="built_in">c</span><span class="punctuation">(</span><span class="string">&quot;right&quot;</span><span class="punctuation">,</span> <span class="string">&quot;bottom&quot;</span><span class="punctuation">)</span><span class="punctuation">)</span></span><br><span class="line"></span><br><span class="line">dev.off<span class="punctuation">(</span><span class="punctuation">)</span><span class="punctuation">&#125;</span> <span class="comment"># 导出 PDF 结束</span></span><br></pre></td></tr></table></figure>
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