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            <h1 id="seo-header">使用Harmony算法移除批次效应</h1>
            
            
              <div class="markdown-body">
                
                <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/2227.html">conda activate seurat</a></li>
<li>conda install -c bioconda r-harmony -y</li>
</ul>
<h2 id="读取数据"><a href="#读取数据" class="headerlink" title="读取数据"></a>读取数据</h2><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><code class="hljs r">root_path <span class="hljs-operator">=</span> <span class="hljs-string">&quot;.&quot;</span><br>f_read10x <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dirN<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tp_samples <span class="hljs-operator">&lt;-</span> list.files<span class="hljs-punctuation">(</span>file.path<span class="hljs-punctuation">(</span>root_path<span class="hljs-punctuation">,</span> dirN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    tp_dir <span class="hljs-operator">&lt;-</span> file.path<span class="hljs-punctuation">(</span>root_path<span class="hljs-punctuation">,</span> dirN<span class="hljs-punctuation">,</span> tp_samples<span class="hljs-punctuation">)</span><br>    <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>tp_dir<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> tp_samples<br>    scRNA <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>lc_ba <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>tp_dir<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        counts <span class="hljs-operator">&lt;-</span> Read10X<span class="hljs-punctuation">(</span>data.dir <span class="hljs-operator">=</span> tp_dir<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>        scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> CreateSeuratObject<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">,</span> project <span class="hljs-operator">=</span> lc_ba<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><br>        scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> PercentageFeatureSet<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^MT-&quot;</span><span class="hljs-punctuation">)</span><br>        scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.ERCC&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> PercentageFeatureSet<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^ERCC-&quot;</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="质量控制"><a href="#质量控制" class="headerlink" title="质量控制"></a>质量控制</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></pre></td><td class="code"><pre><code class="hljs r">options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">6</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>ggrepel.max.overlaps <span class="hljs-operator">=</span> <span class="hljs-literal">Inf</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>scRNAo <span class="hljs-keyword">in</span> scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    print<span class="hljs-punctuation">(</span>VlnPlot<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;nFeature_RNA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;nCount_RNA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> labs<span class="hljs-punctuation">(</span>title <span class="hljs-operator">=</span> scRNAo<span class="hljs-operator">@</span>project.name<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br><br>scRNA<span class="hljs-operator">$</span>APAP1 <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>scRNA<span class="hljs-operator">$</span>APAP1<span class="hljs-punctuation">,</span> subset <span class="hljs-operator">=</span> nFeature_RNA <span class="hljs-operator">&gt;</span> <span class="hljs-number">200</span> <span class="hljs-operator">&amp;</span> nFeature_RNA <span class="hljs-operator">&lt;</span> <span class="hljs-number">3000</span><span class="hljs-punctuation">)</span><br><br>scRNA <span class="hljs-operator">&lt;-</span> Reduce<span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">)</span> merge<span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> scRNA<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="预处理函数"><a href="#预处理函数" class="headerlink" title="预处理函数"></a>预处理函数</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></pre></td><td class="code"><pre><code class="hljs r">f_ScaleData_RunPCA <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA <span class="hljs-operator">&lt;-</span> FindVariableFeatures<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> selection.method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;vst&quot;</span><span class="hljs-punctuation">,</span> nfeatures <span class="hljs-operator">=</span> <span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br>    lc_all.genes <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><br>    scRNA <span class="hljs-operator">&lt;-</span> ScaleData<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> lc_all.genes<span class="hljs-punctuation">)</span><br><br>    scRNA <span class="hljs-operator">&lt;-</span> RunPCA<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> VariableFeatures<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>ElbowPlot<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> ndims <span class="hljs-operator">=</span> <span class="hljs-number">40</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>harmony<span class="hljs-punctuation">)</span><br>f_RunHarmony <span class="hljs-operator">&lt;-</span>  <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> dims<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span> batchN<span class="hljs-operator">=</span><span class="hljs-string">&quot;batch&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA <span class="hljs-operator">=</span> scRNA <span class="hljs-operator">%&gt;%</span> RunHarmony<span class="hljs-punctuation">(</span>batchN<span class="hljs-punctuation">,</span> plot_convergence <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> max.iter.harmony <span class="hljs-operator">=</span> <span class="hljs-number">30</span><span class="hljs-punctuation">)</span><br>    scRNA <span class="hljs-operator">&lt;-</span> scRNA <span class="hljs-operator">%&gt;%</span> RunUMAP<span class="hljs-punctuation">(</span>reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;harmony&quot;</span><span class="hljs-punctuation">,</span> dims <span class="hljs-operator">=</span> dims<span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="分群函数"><a href="#分群函数" class="headerlink" title="分群函数"></a>分群函数</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><code class="hljs r">f_FindNeighbors <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> resolution <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA <span class="hljs-operator">&lt;-</span> scRNA <span class="hljs-operator">%&gt;%</span> FindNeighbors<span class="hljs-punctuation">(</span>reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;harmony&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span>  FindClusters<span class="hljs-punctuation">(</span>resolution <span class="hljs-operator">=</span> resolution<span class="hljs-punctuation">)</span><br>    scRNA<span class="hljs-punctuation">[[</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;h_resolution_&#x27;</span><span class="hljs-punctuation">,</span> resolution<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Idents<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="查看分群质量"><a href="#查看分群质量" class="headerlink" title="查看分群质量"></a>查看分群质量</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></pre></td><td class="code"><pre><code class="hljs r">f_metaG2G <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">,</span> matrixN<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res  <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    alltype <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>type <span class="hljs-keyword">in</span> alltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">==</span> type<span class="hljs-punctuation">]</span><br>        <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;-&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;.&#x27;</span><span class="hljs-punctuation">,</span>res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br><br>f_br_cluster_f <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_filter <span class="hljs-operator">&lt;-</span> unlist<span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">[[</span>lc_groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    lc_filter <span class="hljs-operator">&lt;-</span> lc_filter<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>lc_filter<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    lc_filter<br><span class="hljs-punctuation">&#125;</span><br><br>f_br_cluster <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">,</span> lc_labelN<span class="hljs-punctuation">,</span> lc_prop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_g <span class="hljs-operator">&lt;-</span> f_metaG2G<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">[[</span>lc_groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    lc_l <span class="hljs-operator">&lt;-</span> sObject<span class="hljs-punctuation">[[</span>lc_labelN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    lc_l<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    res <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> f_br_cluster_f<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">,</span> lc_labelN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>lc_prop<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>Nm <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_g<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            tmp <span class="hljs-operator">&lt;-</span> prop.table<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">[</span>lc_g<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>            res<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>Nm <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_g<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            tmp <span class="hljs-operator">&lt;-</span> table<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">[</span>lc_g<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>            res<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>        <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="标注函数"><a href="#标注函数" class="headerlink" title="标注函数"></a>标注函数</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></pre></td><td class="code"><pre><code class="hljs r">f_add_annotation <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_ids<span class="hljs-punctuation">,</span>lc_metaName<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    Idents<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> sObject<span class="hljs-punctuation">[[</span>lc_metaName<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_ids<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> levels<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span><br>    sObject <span class="hljs-operator">&lt;-</span> RenameIdents<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_ids<span class="hljs-punctuation">)</span><br>    sObject<span class="hljs-punctuation">[[</span>lc_metaName<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Idents<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span><br>    sObject<br><span class="hljs-punctuation">&#125;</span><br><br>f_mergeMeta_pre <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> baseMetaN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>baseMetaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br>f_mergeMeta <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> metaData<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>metaData<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>metaData<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br>f_mergeMeta_end <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> as.factor<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
                
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