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            <h1 id="seo-header">通过conda安装纯净环境的cellphoneDB</h1>
            
            
              <div class="markdown-body">
                
                <p><a target="_blank" rel="noopener" href="https://github.com/ventolab/CellphoneDB">https://github.com/ventolab/CellphoneDB</a></p>
<ul>
<li>conda create -n cpdb python&#x3D;3.7 -y</li>
<li>conda activate cpdb</li>
<li>pip install cellphonedb</li>
<li>cellphonedb database list_remote</li>
<li>cellphonedb database download</li>
<li>cellphonedb database list_local</li>
<li>whereis cellphonedb</li>
<li>pip install markupsafe&#x3D;&#x3D;2.0.1</li>
<li>conda deactivate</li>
<li>rm -rf &#x2F;opt&#x2F;conda&#x2F;pkgs&#x2F;r-base-4.1.3-h06d3f91_1</li>
<li>conda create -n cpdb_plot -c conda-forge r-base&#x3D;4.1.3 -y</li>
<li>conda activate cpdb_plot</li>
<li>conda install -c conda-forge r-pheatmap&#x3D;1.0.12 -y</li>
<li>conda install -c conda-forge r-ggplot2&#x3D;3.3.5 -y</li>
<li>whereis R</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><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">f_cpdb_prepare <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_scRNA<span class="hljs-punctuation">,</span> lc_dir<span class="hljs-punctuation">,</span> lc_className<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span><span class="hljs-operator">!</span>file.exists<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>dir.create<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-comment"># 生成 count.txt </span><br>    write.table<span class="hljs-punctuation">(</span>as.matrix<span class="hljs-punctuation">(</span>lc_scRNA<span class="hljs-operator">@</span>assays<span class="hljs-operator">$</span>RNA<span class="hljs-operator">@</span>data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> file.path<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;cellphonedb_count.txt&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sep<span class="hljs-operator">=</span><span class="hljs-string">&#x27;\t&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">quote</span><span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment"># 生成 meta.txt</span><br>    lc_meta_data <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>rownames<span class="hljs-punctuation">(</span>lc_scRNA<span class="hljs-operator">@</span>meta.data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> lc_scRNA<span class="hljs-operator">@</span>meta.data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> lc_className<span class="hljs-punctuation">,</span> drop<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    lc_meta_data <span class="hljs-operator">&lt;-</span> as.matrix<span class="hljs-punctuation">(</span>lc_meta_data<span class="hljs-punctuation">)</span><br>    lc_meta_data<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>lc_meta_data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-string">&quot;Unkown&quot;</span> <span class="hljs-comment">#  细胞类型中不能有NA</span><br>    write.table<span class="hljs-punctuation">(</span>lc_meta_data<span class="hljs-punctuation">,</span> file.path<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;cellphonedb_meta.txt&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sep<span class="hljs-operator">=</span><span class="hljs-string">&#x27;\t&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">quote</span><span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> row.names<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br></pre></td><td class="code"><pre><code class="hljs r">f_cpdb_run <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">,</span> cpdb_Path <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;/opt/conda/envs/cpdb/bin/cellphonedb&#x27;</span><span class="hljs-punctuation">,</span> lc_R_HOME <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;/opt/conda/envs/cpdb_plot/lib/R&#x27;</span><span class="hljs-punctuation">,</span> threads<span class="hljs-operator">=</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tmp_w <span class="hljs-operator">&lt;-</span> getwd<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    setwd<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">)</span><br>    Sys.setenv<span class="hljs-punctuation">(</span>R_HOME <span class="hljs-operator">=</span> lc_R_HOME<span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>Sys.getenv<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;R_HOME&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>system<span class="hljs-punctuation">(</span>command <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;ls&#x27;</span><span class="hljs-punctuation">,</span> intern <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>system<span class="hljs-punctuation">(</span>command <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span>cpdb_Path<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; database list_local&#x27;</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><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>system<span class="hljs-punctuation">(</span>command <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span>cpdb_Path<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; method statistical_analysis  cellphonedb_meta.txt  cellphonedb_count.txt --counts-data=gene_name  --threads=&#x27;</span><span class="hljs-punctuation">,</span> threads<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><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>system<span class="hljs-punctuation">(</span>command <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span>cpdb_Path<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; plot dot_plot&#x27;</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><span class="hljs-punctuation">)</span><br>    print<span class="hljs-punctuation">(</span>system<span class="hljs-punctuation">(</span>command <span class="hljs-operator">=</span> paste0<span class="hljs-punctuation">(</span>cpdb_Path<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27; plot heatmap_plot cellphonedb_meta.txt&#x27;</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><span class="hljs-punctuation">)</span><br>    setwd<span class="hljs-punctuation">(</span>tmp_w<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><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></pre></td><td class="code"><pre><code class="hljs r"><span class="hljs-comment"># Rearrange data column sequence</span><br>require<span class="hljs-punctuation">(</span>tidyverse<span class="hljs-punctuation">)</span><br>f_cDB_order_sequence <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    da <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    df <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>lc_df<span class="hljs-punctuation">,</span> receptor_a <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;True&#x27;</span> <span class="hljs-operator">&amp;</span> receptor_b <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;False&#x27;</span>  receptor_a <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;False&#x27;</span> <span class="hljs-operator">&amp;</span> receptor_b <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;True&#x27;</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>i <span class="hljs-keyword">in</span> <span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>gene_a<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    sub_data <span class="hljs-operator">&lt;-</span> df<span class="hljs-punctuation">[</span>i<span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>sub_data<span class="hljs-operator">$</span>receptor_b<span class="hljs-operator">==</span><span class="hljs-string">&#x27;False&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>sub_data<span class="hljs-operator">$</span>receptor_a<span class="hljs-operator">==</span><span class="hljs-string">&#x27;True&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>            old_names <span class="hljs-operator">&lt;-</span> colnames<span class="hljs-punctuation">(</span>sub_data<span class="hljs-punctuation">)</span><br>            my_list <span class="hljs-operator">&lt;-</span> strsplit<span class="hljs-punctuation">(</span>old_names<span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">11</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> split<span class="hljs-operator">=</span><span class="hljs-string">&quot;\\&quot;</span><span class="hljs-punctuation">)</span><br>            my_character <span class="hljs-operator">&lt;-</span> paste<span class="hljs-punctuation">(</span>sapply<span class="hljs-punctuation">(</span>my_list<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;[[&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-number">2L</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sapply<span class="hljs-punctuation">(</span>my_list<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;[[&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1L</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> sep<span class="hljs-operator">=</span><span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">)</span><br>            new_names <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>sub_data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">4</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;gene_b&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;gene_a&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;secreted&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;receptor_b&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;receptor_a&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;annotation_strategy&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;is_integrin&quot;</span><span class="hljs-punctuation">,</span> my_character<span class="hljs-punctuation">)</span><br>            sub_data <span class="hljs-operator">=</span> dplyr<span class="hljs-operator">::</span>select<span class="hljs-punctuation">(</span>sub_data<span class="hljs-punctuation">,</span> new_names<span class="hljs-punctuation">)</span><br>            <span class="hljs-comment"># print(&#x27;Change sequence!!!&#x27;)</span><br>            <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>sub_data<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> old_names<br>            da <span class="hljs-operator">=</span> rbind<span class="hljs-punctuation">(</span>da<span class="hljs-punctuation">,</span> sub_data<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>            da <span class="hljs-operator">=</span> rbind<span class="hljs-punctuation">(</span>da<span class="hljs-punctuation">,</span> sub_data<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>da<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br> <br>f_cDB_mergePandM <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>means_order<span class="hljs-punctuation">,</span> pvals_order<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    means_sub <span class="hljs-operator">&lt;-</span> means_order<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;interacting_pair&#x27;</span><span class="hljs-punctuation">,</span> colnames<span class="hljs-punctuation">(</span>means_order<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">11</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    pvals_sub <span class="hljs-operator">&lt;-</span> pvals_order<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;interacting_pair&#x27;</span><span class="hljs-punctuation">,</span> colnames<span class="hljs-punctuation">(</span>means_order<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">11</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    means_gather <span class="hljs-operator">&lt;-</span> tidyr<span class="hljs-operator">::</span>gather<span class="hljs-punctuation">(</span>means_sub<span class="hljs-punctuation">,</span> celltype<span class="hljs-punctuation">,</span> mean_expression<span class="hljs-punctuation">,</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>means_sub<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    pvals_gather <span class="hljs-operator">&lt;-</span> tidyr<span class="hljs-operator">::</span>gather<span class="hljs-punctuation">(</span>pvals_sub<span class="hljs-punctuation">,</span> celltype<span class="hljs-punctuation">,</span> pval<span class="hljs-punctuation">,</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>pvals_sub<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    mean_pval <span class="hljs-operator">&lt;-</span> dplyr<span class="hljs-operator">::</span>left_join<span class="hljs-punctuation">(</span>means_gather<span class="hljs-punctuation">,</span> pvals_gather<span class="hljs-punctuation">,</span> by <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;interacting_pair&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;celltype&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    mean_pval<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br></pre></td><td class="code"><pre><code class="hljs r">f_readcellphoneDB <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    res <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>pvals <span class="hljs-operator">&lt;-</span> f_cDB_order_sequence<span class="hljs-punctuation">(</span>read.delim<span class="hljs-punctuation">(</span>file.path<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;out&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;pvalues.txt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> check.names <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>means <span class="hljs-operator">&lt;-</span> f_cDB_order_sequence<span class="hljs-punctuation">(</span>read.delim<span class="hljs-punctuation">(</span>file.path<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;out&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;means.txt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> check.names <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>s_means <span class="hljs-operator">&lt;-</span> read.delim<span class="hljs-punctuation">(</span>file.path<span class="hljs-punctuation">(</span>lc_dir<span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;out&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;significant_means.txt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> check.names <span class="hljs-operator">=</span> <span class="hljs-literal">FALSE</span><span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>m_p <span class="hljs-operator">&lt;-</span> dplyr<span class="hljs-operator">::</span>distinct<span class="hljs-punctuation">(</span>f_cDB_mergePandM<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>means<span class="hljs-punctuation">,</span> res<span class="hljs-operator">$</span>pvals<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    lc_tp <span class="hljs-operator">&lt;-</span> res<span class="hljs-operator">$</span>m_p <span class="hljs-operator">%&gt;%</span> dplyr<span class="hljs-operator">::</span>select<span class="hljs-punctuation">(</span>interacting_pair<span class="hljs-punctuation">,</span> celltype<span class="hljs-punctuation">,</span> pval<span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> tidyr<span class="hljs-operator">::</span>spread<span class="hljs-punctuation">(</span>key<span class="hljs-operator">=</span>celltype<span class="hljs-punctuation">,</span> value<span class="hljs-operator">=</span>pval<span class="hljs-punctuation">)</span><br>    lc_sig_pairs <span class="hljs-operator">&lt;-</span> lc_tp<span class="hljs-punctuation">[</span>which<span class="hljs-punctuation">(</span>rowSums<span class="hljs-punctuation">(</span>lc_tp<span class="hljs-operator">&lt;=</span><span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><span class="hljs-operator">!=</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-punctuation">]</span><br>    res<span class="hljs-operator">$</span>s_m_p <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>m_p<span class="hljs-punctuation">,</span> interacting_pair <span class="hljs-operator">%in%</span> lc_sig_pairs<span class="hljs-operator">$</span>interacting_pair<span class="hljs-punctuation">)</span><br>    res<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><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></pre></td><td class="code"><pre><code class="hljs r">f_cDB_dotplot <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_m_p<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    lc_m_p <span class="hljs-operator">%&gt;%</span> ggplot<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span>interacting_pair<span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span>celltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    <span class="hljs-comment"># geom_point(aes(color=log2(mean_expression), size=pval)) +</span><br>    <span class="hljs-comment"># scale_size(trans = &#x27;reverse&#x27;) +</span><br>    geom_point<span class="hljs-punctuation">(</span>aes<span class="hljs-punctuation">(</span>color<span class="hljs-operator">=</span>log2<span class="hljs-punctuation">(</span>mean_expression<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> size<span class="hljs-operator">=</span><span class="hljs-operator">-</span>log10<span class="hljs-punctuation">(</span>pval<span class="hljs-operator">+</span><span class="hljs-number">1</span><span class="hljs-operator">*</span><span class="hljs-number">10</span><span class="hljs-operator">^</span><span class="hljs-operator">-</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    guides<span class="hljs-punctuation">(</span>colour <span class="hljs-operator">=</span> guide_colourbar<span class="hljs-punctuation">(</span>order <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>size <span class="hljs-operator">=</span> guide_legend<span class="hljs-punctuation">(</span>order <span class="hljs-operator">=</span> <span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    labs<span class="hljs-punctuation">(</span>x<span class="hljs-operator">=</span><span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-string">&#x27;&#x27;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    scale_color_gradientn<span class="hljs-punctuation">(</span>name<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Expression level \n(log2 mean expression \nmolecule1, molecule2)&#x27;</span><span class="hljs-punctuation">,</span> colours <span class="hljs-operator">=</span> terrain.colors<span class="hljs-punctuation">(</span><span class="hljs-number">100</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    <span class="hljs-comment"># scale_color_gradient2(&#x27;Expression level \n(log2 mean expression \nmolecule1, molecule2)&#x27;, low = &#x27;blue&#x27;, mid = &#x27;yellow&#x27;, high = &#x27;red&#x27;) +</span><br>    theme<span class="hljs-punctuation">(</span>axis.text.x<span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>angle<span class="hljs-operator">=</span><span class="hljs-number">45</span><span class="hljs-punctuation">,</span> hjust<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    <span class="hljs-comment"># coord_flip() +</span><br>    theme<span class="hljs-punctuation">(</span><br>    panel.border <span class="hljs-operator">=</span> element_rect<span class="hljs-punctuation">(</span>color <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;black&#x27;</span><span class="hljs-punctuation">,</span> fill <span class="hljs-operator">=</span> <span class="hljs-literal">NA</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    panel.grid.major.x <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    panel.grid.major.y <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    panel.grid.minor.x <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    panel.grid.minor.y <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    panel.background   <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    axis.title.x       <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    axis.title.y       <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>    axis.ticks         <span class="hljs-operator">=</span> element_blank<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-comment"># plot.title         = element_text(hjust = 0.5),</span><br>    <span class="hljs-comment"># legend.position = &#x27;bottom&#x27; # guides(fill = guide_legend(label.position = &quot;bottom&quot;))</span><br>    <span class="hljs-comment"># legend.position    = &quot;bottom&quot;</span><br>    <span class="hljs-comment"># axis.text.y.right  = element_text(angle=270, hjust=0.5)</span><br>    <span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br>    theme<span class="hljs-punctuation">(</span>legend.key.size <span class="hljs-operator">=</span> unit<span class="hljs-punctuation">(</span><span class="hljs-number">0.4</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;cm&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#change legend key size</span><br>    <span class="hljs-comment"># legend.key.height = unit(1, &#x27;cm&#x27;), #change legend key height</span><br>    <span class="hljs-comment"># legend.key.width = unit(1, &#x27;cm&#x27;), #change legend key width</span><br>    legend.title <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">9</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#change legend title font size</span><br>    legend.text <span class="hljs-operator">=</span> element_text<span class="hljs-punctuation">(</span>size<span class="hljs-operator">=</span><span class="hljs-number">8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#change legend text font size</span><br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>

<h2 id="示例"><a href="#示例" class="headerlink" title="示例"></a>示例</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></pre></td><td class="code"><pre><code class="hljs r">library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span><br>sce <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;~/upload/zl_liu//data//pca.rds&quot;</span><span class="hljs-punctuation">)</span><br>Myeloid <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span>cell_type<span class="hljs-operator">==</span><span class="hljs-string">&quot;Myeloid&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">100</span><span class="hljs-punctuation">]</span><br>f_cpdb_prepare<span class="hljs-punctuation">(</span>lc_scRNA <span class="hljs-operator">=</span> Myeloid<span class="hljs-punctuation">,</span> lc_dir <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Myeloid_100&#x27;</span><span class="hljs-punctuation">,</span> lc_className <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;cell_type_fig1spA&#x27;</span><span class="hljs-punctuation">)</span><br>f_cpdb_run<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Myeloid_100&#x27;</span><span class="hljs-punctuation">)</span><br>br_d <span class="hljs-operator">&lt;-</span> f_readcellphoneDB<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;Myeloid_100&#x27;</span><span class="hljs-punctuation">)</span><br>tp_img <span class="hljs-operator">&lt;-</span> f_cDB_dotplot<span class="hljs-punctuation">(</span>subset<span class="hljs-punctuation">(</span>br_d <span class="hljs-operator">$</span>s_m_p<span class="hljs-punctuation">,</span> pval<span class="hljs-operator">&lt;</span><span class="hljs-number">0.05</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>tp_img<br></code></pre></td></tr></table></figure>
                
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