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            <h1 id="seo-header">scran：使用fastMNN算法移除批次效应</h1>
            
            
              <div class="markdown-body">
                
                <p>为了复现<a target="_blank" rel="noopener" href="https://www.nature.com/articles/s41556-020-00613-6">这篇Nature Cell Biology上文章</a>的结果，试试文章提供的代码</p>
<h2 id="安装补充包"><a href="#安装补充包" class="headerlink" title="安装补充包"></a>安装补充包</h2><ul>
<li><a href="https://occdn.limour.top/1534.html">conda activate seurat</a></li>
<li>conda install -c bioconda bioconductor-scran -y</li>
<li>conda install -c bioconda bioconductor-scater -y</li>
<li>install.packages(“BoutrosLab.plotting.general”)</li>
<li>conda install -c bioconda bioconductor-batchelor -y</li>
<li># conda install -c bioconda bioconductor-biocparallel -y</li>
</ul>
<h2 id="读入UMI矩阵-已QC"><a href="#读入UMI矩阵-已QC" class="headerlink" title="读入UMI矩阵(已QC)"></a>读入UMI矩阵(已QC)</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br></pre></td><td class="code"><pre><code class="hljs R">scRNA <span class="hljs-operator">&lt;-</span> read.table<span class="hljs-punctuation">(</span> gzfile<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;GSM4203181/GSM4203181_data.raw.matrix.txt.gz&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> header <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="构建SingleCellExperiment"><a href="#构建SingleCellExperiment" class="headerlink" title="构建SingleCellExperiment"></a>构建SingleCellExperiment</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><code class="hljs R">library<span class="hljs-punctuation">(</span>scran<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>scater<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>batchelor<span class="hljs-punctuation">)</span>;<br>sce <span class="hljs-operator">&lt;-</span> SingleCellExperiment<span class="hljs-punctuation">(</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>counts<span class="hljs-operator">=</span>scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">$</span>batch <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;sample&#x27;</span><span class="hljs-punctuation">,</span>substr<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-number">18</span><span class="hljs-punctuation">,</span>nchar<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>by.lib <span class="hljs-operator">&lt;-</span> split<span class="hljs-punctuation">(</span><span class="hljs-built_in">seq_len</span><span class="hljs-punctuation">(</span>ncol<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sce<span class="hljs-operator">$</span>batch<span class="hljs-punctuation">)</span>;<br>cluster.id <span class="hljs-operator">&lt;-</span> character<span class="hljs-punctuation">(</span>ncol<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>lib <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>by.lib<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-punctuation">&#123;</span> <br>    print<span class="hljs-punctuation">(</span>lib<span class="hljs-punctuation">)</span><br>    current <span class="hljs-operator">&lt;-</span> by.lib<span class="hljs-punctuation">[[</span>lib<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    cur.exprs <span class="hljs-operator">&lt;-</span> realize<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>current<span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># for speed; avoid multiple file reads here.</span><br>    ids <span class="hljs-operator">&lt;-</span> quickCluster<span class="hljs-punctuation">(</span>cur.exprs<span class="hljs-punctuation">,</span> min.mean<span class="hljs-operator">=</span><span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span> method<span class="hljs-operator">=</span><span class="hljs-string">&quot;igraph&quot;</span><span class="hljs-punctuation">)</span><br>    cluster.id<span class="hljs-punctuation">[</span>current<span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span>lib<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;.&quot;</span><span class="hljs-punctuation">,</span> ids<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>sce <span class="hljs-operator">&lt;-</span> computeSumFactors<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> cluster<span class="hljs-operator">=</span>cluster.id<span class="hljs-punctuation">,</span> min.mean<span class="hljs-operator">=</span><span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span> max.cluster.size<span class="hljs-operator">=</span><span class="hljs-number">3000</span><span class="hljs-punctuation">)</span>;<br>sce <span class="hljs-operator">&lt;-</span> logNormCounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span>;<br>saveRDS<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;clustered_normalized.rds&#x27;</span><span class="hljs-punctuation">)</span>;<br></code></pre></td></tr></table></figure>

<h2 id="运行MNN"><a href="#运行MNN" class="headerlink" title="运行MNN"></a>运行MNN</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>scran<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>scater<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>batchelor<span class="hljs-punctuation">)</span>;<br>sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;clustered_normalized.rds&#x27;</span><span class="hljs-punctuation">)</span><br>batch <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>as.factor<span class="hljs-punctuation">(</span>sce<span class="hljs-operator">$</span>batch<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>count1 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span>;<br>count2 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">2</span><span class="hljs-punctuation">]</span>;<br>count3 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">3</span><span class="hljs-punctuation">]</span>;<br>count4 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">4</span><span class="hljs-punctuation">]</span>;<br>count5 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">5</span><span class="hljs-punctuation">]</span>;<br>count6 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">6</span><span class="hljs-punctuation">]</span>;<br>count7 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">7</span><span class="hljs-punctuation">]</span>;<br>count8 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">8</span><span class="hljs-punctuation">]</span>;<br>count9 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">9</span><span class="hljs-punctuation">]</span>;<br>count10 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">10</span><span class="hljs-punctuation">]</span>;<br>count11 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">11</span><span class="hljs-punctuation">]</span>;<br>count12 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">12</span><span class="hljs-punctuation">]</span>;<br>count13 <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> batch <span class="hljs-operator">==</span> <span class="hljs-number">13</span><span class="hljs-punctuation">,</span> drop <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">]</span>;<br>original <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>count1<span class="hljs-punctuation">,</span> count2<span class="hljs-punctuation">,</span> count3<span class="hljs-punctuation">,</span> count4<span class="hljs-punctuation">,</span> count5<span class="hljs-punctuation">,</span> count6<span class="hljs-punctuation">,</span> count7<span class="hljs-punctuation">,</span> count8<span class="hljs-punctuation">,</span><br>    count9<span class="hljs-punctuation">,</span> count10<span class="hljs-punctuation">,</span> count11<span class="hljs-punctuation">,</span> count12<span class="hljs-punctuation">,</span> count13<span class="hljs-punctuation">)</span>;<br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>original<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> levels<span class="hljs-punctuation">(</span>as.factor<span class="hljs-punctuation">(</span>as.factor<span class="hljs-punctuation">(</span>sce<span class="hljs-operator">$</span>batch<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>gc<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>system<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;python3 /home/jovyan/upload/zl_liu/wecomchan.py&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;&#x27;fastMNN_task start&#x27;&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> intern <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>out  <span class="hljs-operator">&lt;-</span>  tryCatch<span class="hljs-punctuation">(</span><span class="hljs-punctuation">&#123;</span><br>      <span class="hljs-comment">#正常的逻辑</span><br>    do.call<span class="hljs-punctuation">(</span>fastMNN<span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>original<span class="hljs-punctuation">,</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>k <span class="hljs-operator">=</span> <span class="hljs-number">20</span><span class="hljs-punctuation">,</span> d <span class="hljs-operator">=</span> <span class="hljs-number">50</span><span class="hljs-punctuation">,</span> BPPARAM <span class="hljs-operator">=</span> BiocParallel<span class="hljs-operator">::</span>MulticoreParam<span class="hljs-punctuation">(</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>  <span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">,</span> warning <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>w<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">&#123;</span><br>      <span class="hljs-comment">#出现warning的处理逻辑</span><br>    w <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>w<span class="hljs-punctuation">)</span><br>    w <span class="hljs-operator">&lt;-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;[\r\n&#x27;]&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> w<span class="hljs-punctuation">)</span><br>    system<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;python3 /home/jovyan/upload/zl_liu/wecomchan.py&quot;</span><span class="hljs-punctuation">,</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;&#x27;&quot;</span><span class="hljs-punctuation">,</span>w<span class="hljs-punctuation">,</span><span class="hljs-string">&quot;&#x27;&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> intern <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>    w<br>  <span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">,</span> error <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>e<span class="hljs-punctuation">)</span> <span class="hljs-punctuation">&#123;</span><br>      <span class="hljs-comment">#出现error的处理逻辑</span><br>    e <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>e<span class="hljs-punctuation">)</span><br>    e <span class="hljs-operator">&lt;-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;[\r\n&#x27;]&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;&quot;</span><span class="hljs-punctuation">,</span> e<span class="hljs-punctuation">)</span><br>    system<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;python3 /home/jovyan/upload/zl_liu/wecomchan.py&quot;</span><span class="hljs-punctuation">,</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;&#x27;&quot;</span><span class="hljs-punctuation">,</span>e<span class="hljs-punctuation">,</span><span class="hljs-string">&quot;&#x27;&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> intern <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>    e<br>  <span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">,</span> finally <span class="hljs-operator">=</span> <span class="hljs-punctuation">&#123;</span><br>      <span class="hljs-comment">#不管出现异常还是正常都会执行的代码模块，</span><br>      <span class="hljs-comment">#一般用来处理清理操作，例如关闭连接资源等。</span><br><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>system<span class="hljs-punctuation">(</span>paste<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;python3 /home/jovyan/upload/zl_liu/wecomchan.py&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;&#x27;fastMNN completed&#x27;&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> intern <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="创建sce"><a href="#创建sce" class="headerlink" title="创建sce"></a>创建sce</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs R">combined <span class="hljs-operator">&lt;-</span> do.call<span class="hljs-punctuation">(</span>cbind<span class="hljs-punctuation">,</span> original<span class="hljs-punctuation">)</span>;<br>sce <span class="hljs-operator">&lt;-</span> SingleCellExperiment<span class="hljs-punctuation">(</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>logcounts <span class="hljs-operator">=</span> combined<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span>;<br>reducedDim<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;MNN&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> reducedDim<span class="hljs-punctuation">(</span>out<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;corrected&#x27;</span><span class="hljs-punctuation">)</span><br>sce<span class="hljs-operator">$</span>Batch <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;sample&#x27;</span><span class="hljs-punctuation">,</span>substr<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-number">18</span><span class="hljs-punctuation">,</span>nchar<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>gc<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;sce.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="合并sce到seurat"><a href="#合并sce到seurat" class="headerlink" title="合并sce到seurat"></a>合并sce到seurat</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>scran<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>scater<span class="hljs-punctuation">)</span>;<br>library<span class="hljs-punctuation">(</span>batchelor<span class="hljs-punctuation">)</span>;<br>scRNA <span class="hljs-operator">&lt;-</span> read.table<span class="hljs-punctuation">(</span> gzfile<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;GSM4203181/GSM4203181_data.raw.matrix.txt.gz&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> header <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> row.names <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;sce.rds&#x27;</span><span class="hljs-punctuation">)</span><br>count.log <span class="hljs-operator">&lt;-</span> logcounts<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">)</span><br>scRNA <span class="hljs-operator">&lt;-</span> scRNA<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>count.log<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>colnames<span class="hljs-punctuation">(</span>count.log<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>tmp <span class="hljs-operator">&lt;-</span> SingleCellExperiment<span class="hljs-punctuation">(</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>counts<span class="hljs-operator">=</span>scRNA<span class="hljs-punctuation">,</span> logcounts<span class="hljs-operator">=</span>count.log<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>tmp<span class="hljs-operator">$</span>Batch <span class="hljs-operator">&lt;-</span> sce<span class="hljs-operator">$</span>Batch<br>reducedDim<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;MNN&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> reducedDim<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;MNN&#x27;</span><span class="hljs-punctuation">)</span><br>saveRDS<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;scRNA.rds&#x27;</span><span class="hljs-punctuation">)</span><br>as.Seurat<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="画图看看效果"><a href="#画图看看效果" class="headerlink" title="画图看看效果"></a>画图看看效果</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs R">sce <span class="hljs-operator">&lt;-</span> runTSNE<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> use_dimred<span class="hljs-operator">=</span><span class="hljs-string">&quot;MNN&quot;</span><span class="hljs-punctuation">)</span>;<br>plotTSNE<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> colour_by<span class="hljs-operator">=</span><span class="hljs-string">&quot;Batch&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<p><img src="https://img-cdn.limour.top/2022/08/13/62f7500076865.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload></p>
<p>效果稀碎。。。</p>

                
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