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            <h1 id="seo-header">对富集结果进行贝叶斯网络推断</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/2126.html">conda activate clusterprofiler</a></li>
<li>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json &amp;</li>
<li>wget -e “https_proxy&#x3D;<a target="_blank" rel="noopener" href="http://127.0.0.1:20809/">http://127.0.0.1:20809</a>“ <a target="_blank" rel="noopener" href="https://github.com/noriakis/CBNplot/archive/refs/heads/main.zip">https://github.com/noriakis/CBNplot/archive/refs/heads/main.zip</a> -O CBNplot-master.zip</li>
<li>conda install -c conda-forge r-rmpfr -y</li>
<li># conda install -c bioconda bioconductor-depmap -y</li>
<li>BiocManager::install(“depmap”, force &#x3D; TRUE)</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></pre></td><td class="code"><pre><code class="hljs R">dep <span class="hljs-operator">=</span> depmap<span class="hljs-operator">::</span>depmap_crispr<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>rnai <span class="hljs-operator">=</span> depmap<span class="hljs-operator">::</span>depmap_rnai<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>depMeta <span class="hljs-operator">=</span> depmap<span class="hljs-operator">::</span>depmap_metadata<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>save<span class="hljs-punctuation">(</span>dep<span class="hljs-punctuation">,</span> rnai<span class="hljs-punctuation">,</span> depMeta<span class="hljs-punctuation">,</span> file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;~/upload/zl_liu/gsea/CBNplot_depmap.rdata&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<ul>
<li>devtools::install_local(‘CBNplot-master.zip’)</li>
</ul>
<h2 id="准备数据"><a href="#准备数据" class="headerlink" title="准备数据"></a>准备数据</h2><ul>
<li><a href="https://occdn.limour.top/2132.html">差异基因</a>、<a href="https://occdn.limour.top/2197.html">有批次的差异基因</a></li>
<li><a href="https://occdn.limour.top/2190.html">通路富集Demo</a></li>
<li><a href="https://occdn.limour.top/2195.html">表达矩阵标准化</a>，emm，这个包有bug，exp矩阵的基因不能是SYMBOL，还得折腾。</li>
</ul>
<h3 id="折腾exp矩阵的基因ID"><a href="#折腾exp矩阵的基因ID" class="headerlink" title="折腾exp矩阵的基因ID"></a>折腾exp矩阵的基因ID</h3><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br><span class="line">22</span><br><span class="line">23</span><br><span class="line">24</span><br><span class="line">25</span><br><span class="line">26</span><br><span class="line">27</span><br><span class="line">28</span><br><span class="line">29</span><br><span class="line">30</span><br><span class="line">31</span><br><span class="line">32</span><br><span class="line">33</span><br><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br><span class="line">37</span><br><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br><span class="line">46</span><br><span class="line">47</span><br><span class="line">48</span><br><span class="line">49</span><br><span class="line">50</span><br><span class="line">51</span><br><span class="line">52</span><br><span class="line">53</span><br><span class="line">54</span><br><span class="line">55</span><br><span class="line">56</span><br><span class="line">57</span><br></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>SummarizedExperiment<span class="hljs-punctuation">)</span><br>tmp <span class="hljs-operator">&lt;-</span> load<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../DEG/TCGA/PRAD_tp.rda&#x27;</span><span class="hljs-punctuation">)</span><br>counts <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>assays<span class="hljs-operator">@</span>data<span class="hljs-operator">$</span>unstranded<br>colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> data<span class="hljs-operator">@</span>colData<span class="hljs-operator">$</span>patient<br>f_rm_duplicated <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">,</span> reverse<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    tmp <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>NameL<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>reverse<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">&gt;</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br>        tmp <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-operator">$</span>NameL<span class="hljs-punctuation">[</span>tmp<span class="hljs-operator">$</span>Freq <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">]</span><br>    <span class="hljs-punctuation">&#125;</span><br>    which<span class="hljs-punctuation">(</span>NameL <span class="hljs-operator">%in%</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>counts <span class="hljs-operator">&lt;-</span> counts<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>f_rm_duplicated<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>geneInfo <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>data<span class="hljs-operator">@</span>rowRanges<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;gene_id&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_type&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;gene_name&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>f_dedup_IQR <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> rowNn<span class="hljs-punctuation">,</span> select_func<span class="hljs-operator">=</span><span class="hljs-string">&#x27;IQR&#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>typeof<span class="hljs-punctuation">(</span>select_func<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-string">&#x27;character&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        select_func <span class="hljs-operator">=</span> get<span class="hljs-punctuation">(</span>select_func<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    <span class="hljs-comment"># 拆出无重复的数据，后续不进行处理</span><br>    noDup <span class="hljs-operator">&lt;-</span> f_rm_duplicated<span class="hljs-punctuation">(</span>rowNn<span class="hljs-punctuation">)</span><br>    tmp <span class="hljs-operator">&lt;-</span> rowNn<span class="hljs-punctuation">[</span>noDup<span class="hljs-punctuation">]</span><br>    noDup <span class="hljs-operator">&lt;-</span> df<span class="hljs-punctuation">[</span>noDup<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>noDup<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> tmp<br>    <span class="hljs-comment"># 拆除有重复的数据</span><br>    Dup <span class="hljs-operator">&lt;-</span> f_rm_duplicated<span class="hljs-punctuation">(</span>rowNn<span class="hljs-punctuation">,</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br>    rowNn <span class="hljs-operator">&lt;-</span> rowNn<span class="hljs-punctuation">[</span>Dup<span class="hljs-punctuation">]</span><br>    Dup <span class="hljs-operator">&lt;-</span> df<span class="hljs-punctuation">[</span>Dup<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>Dup<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>    <span class="hljs-comment"># 处理重复的数据</span><br>    lc_tmp <span class="hljs-operator">=</span> by<span class="hljs-punctuation">(</span>Dup<span class="hljs-punctuation">,</span><br>         rowNn<span class="hljs-punctuation">,</span><br>         <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span>rownames<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>which.max<span class="hljs-punctuation">(</span>apply<span class="hljs-punctuation">(</span>X <span class="hljs-operator">=</span> x<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> select_func<span class="hljs-punctuation">,</span> MARGIN <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">)</span><br>    lc_probes <span class="hljs-operator">=</span> <span class="hljs-built_in">as.integer</span><span class="hljs-punctuation">(</span>lc_tmp<span class="hljs-punctuation">)</span><br>    Dup <span class="hljs-operator">=</span> Dup<span class="hljs-punctuation">[</span>lc_probes<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>    rownames<span class="hljs-punctuation">(</span>Dup<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> rowNn<span class="hljs-punctuation">[</span>lc_probes<span class="hljs-punctuation">]</span><br>    <span class="hljs-comment"># 合并数据并返回</span><br>    <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span>rbind<span class="hljs-punctuation">(</span>noDup<span class="hljs-punctuation">,</span>Dup<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>stringr<span class="hljs-punctuation">)</span><br>rininiang <span class="hljs-operator">&lt;-</span> t<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>str_split<span class="hljs-punctuation">(</span>geneInfo<span class="hljs-operator">$</span>gene_id<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;\\.&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>rownames<span class="hljs-punctuation">(</span>rininiang<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>rininiang <span class="hljs-operator">&lt;-</span> f_dedup_IQR<span class="hljs-punctuation">(</span>as.data.frame<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>unlist<span class="hljs-punctuation">(</span>rininiang<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>rininiang<br>f_counts2VST <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>countsMatrix<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    require<span class="hljs-punctuation">(</span>DESeq2<span class="hljs-punctuation">)</span><br>    conditions <span class="hljs-operator">&lt;-</span> factor<span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Control&quot;</span><span class="hljs-punctuation">,</span>ncol<span class="hljs-punctuation">(</span>countsMatrix<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    colData_b <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>countsMatrix<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> conditions<span class="hljs-punctuation">)</span><br>    dds <span class="hljs-operator">&lt;-</span> DESeqDataSetFromMatrix<span class="hljs-punctuation">(</span>countData <span class="hljs-operator">=</span> countsMatrix<span class="hljs-punctuation">,</span><br>                              colData <span class="hljs-operator">=</span> colData_b<span class="hljs-punctuation">,</span><br>                              design <span class="hljs-operator">=</span> <span class="hljs-operator">~</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    vsd <span class="hljs-operator">&lt;-</span> vst<span class="hljs-punctuation">(</span>object<span class="hljs-operator">=</span>dds<span class="hljs-punctuation">,</span> blind<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span> <br>    assay<span class="hljs-punctuation">(</span>vsd<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>VST <span class="hljs-operator">&lt;-</span> f_counts2VST<span class="hljs-punctuation">(</span>rininiang<span class="hljs-punctuation">)</span><br>VST<br>saveRDS<span class="hljs-punctuation">(</span>VST<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;rininiang.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="折腾通路的名称大小写"><a href="#折腾通路的名称大小写" class="headerlink" title="折腾通路的名称大小写"></a>折腾通路的名称大小写</h3><ul>
<li>~&#x2F;dev&#x2F;xray&#x2F;xray -c ~&#x2F;etc&#x2F;xui2.json</li>
<li>Sys.setenv(http_proxy &#x3D; “<a target="_blank" rel="noopener" href="http://127.0.0.1:20809/">http://127.0.0.1:20809</a>“)</li>
<li>Sys.setenv(https_proxy &#x3D; “<a target="_blank" rel="noopener" href="http://127.0.0.1:20809/">http://127.0.0.1:20809</a>“)</li>
</ul>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br></pre></td><td class="code"><pre><code class="hljs R">rininiang <span class="hljs-operator">&lt;-</span> graphite<span class="hljs-operator">::</span>pathways<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;hsapiens&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;reactome&#x27;</span><span class="hljs-punctuation">)</span><br>pway<span class="hljs-operator">@</span>result<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Description&quot;</span><span class="hljs-punctuation">]</span><br>rininiang<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Cell Cycle&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br>pway<span class="hljs-operator">@</span>result<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;Description&quot;</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;Cell Cycle&#x27;</span><br></code></pre></td></tr></table></figure>

<h2 id="推断基因"><a href="#推断基因" class="headerlink" title="推断基因"></a>推断基因</h2><h3 id="准备画图"><a href="#准备画图" class="headerlink" title="准备画图"></a>准备画图</h3><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">require<span class="hljs-punctuation">(</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br>set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">123</span><span class="hljs-punctuation">)</span><br>bngeneplot<span class="hljs-punctuation">(</span>results <span class="hljs-operator">=</span> pway<span class="hljs-punctuation">,</span> <span class="hljs-built_in">exp</span> <span class="hljs-operator">=</span> vsted<span class="hljs-punctuation">,</span> expSample <span class="hljs-operator">=</span> incSample<span class="hljs-punctuation">,</span> R <span class="hljs-operator">=</span> <span class="hljs-number">200</span><span class="hljs-punctuation">,</span> cl <span class="hljs-operator">=</span> cl<span class="hljs-punctuation">,</span><br>           pathNum <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>           strThresh <span class="hljs-operator">=</span> <span class="hljs-number">0.8</span><span class="hljs-punctuation">,</span><br>           showDir <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br>           hub<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span> <br><span class="hljs-comment">#             sizeDep = T, dep = dep, cellLineName = &quot;UMUC3_URINARY_TRACT&quot;, showLineage = T, depMeta = depMeta,</span><br>           pathDb <span class="hljs-operator">=</span> <span class="hljs-string">&quot;reactome&quot;</span><span class="hljs-punctuation">,</span>  compareRef <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> compareRefType <span class="hljs-operator">=</span> <span class="hljs-string">&quot;difference&quot;</span><span class="hljs-punctuation">,</span><br>           labelSize<span class="hljs-operator">=</span><span class="hljs-number">7</span><span class="hljs-punctuation">,</span> shadowText<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> <br>           expRow<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ENSEMBL&#x27;</span><span class="hljs-punctuation">,</span> convertSymbol<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> orgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">,</span> sp <span class="hljs-operator">=</span> <span class="hljs-string">&quot;hsapiens&quot;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="另一种风格"><a href="#另一种风格" class="headerlink" title="另一种风格"></a>另一种风格</h3><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">set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">123</span><span class="hljs-punctuation">)</span><br>bngeneplotCustom<span class="hljs-punctuation">(</span>results <span class="hljs-operator">=</span> pway<span class="hljs-punctuation">,</span> <span class="hljs-built_in">exp</span> <span class="hljs-operator">=</span> vsted<span class="hljs-punctuation">,</span> expSample <span class="hljs-operator">=</span> incSample<span class="hljs-punctuation">,</span> R <span class="hljs-operator">=</span> <span class="hljs-number">200</span><span class="hljs-punctuation">,</span> cl <span class="hljs-operator">=</span> cl<span class="hljs-punctuation">,</span><br>           pathNum <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>           strThresh <span class="hljs-operator">=</span> <span class="hljs-number">0.8</span><span class="hljs-punctuation">,</span><br>           showDir <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br>           hub<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span> <br>           expRow<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ENSEMBL&#x27;</span><span class="hljs-punctuation">,</span> convertSymbol<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> orgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">,</span><br>           layout<span class="hljs-operator">=</span><span class="hljs-string">&quot;nicely&quot;</span><span class="hljs-punctuation">,</span> fontFamily<span class="hljs-operator">=</span><span class="hljs-string">&quot;sans&quot;</span><span class="hljs-punctuation">,</span> strType<span class="hljs-operator">=</span><span class="hljs-string">&quot;normal&quot;</span><span class="hljs-punctuation">,</span> glowEdgeNum<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span>  labelSize<span class="hljs-operator">=</span><span class="hljs-number">7</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="推断通路"><a href="#推断通路" class="headerlink" title="推断通路"></a>推断通路</h2><ul>
<li>改回折腾通路的名称大小写中通路的名字</li>
</ul>
<figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br></pre></td><td class="code"><pre><code class="hljs R">bnpathplot<span class="hljs-punctuation">(</span>results <span class="hljs-operator">=</span> pway<span class="hljs-punctuation">,</span> <span class="hljs-built_in">exp</span> <span class="hljs-operator">=</span> vsted<span class="hljs-punctuation">,</span> expSample <span class="hljs-operator">=</span> incSample<span class="hljs-punctuation">,</span> R <span class="hljs-operator">=</span> <span class="hljs-number">200</span><span class="hljs-punctuation">,</span><br>           nCategory <span class="hljs-operator">=</span> <span class="hljs-number">5</span><span class="hljs-punctuation">,</span><br>           expRow<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ENSEMBL&#x27;</span><span class="hljs-punctuation">,</span> orgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="Reactome"><a href="#Reactome" class="headerlink" title="Reactome"></a>Reactome</h3><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">pway<span class="hljs-operator">@</span>ontology <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Reactome&#x27;</span><br>bnpathplot<span class="hljs-punctuation">(</span>results <span class="hljs-operator">=</span> pway<span class="hljs-punctuation">,</span> <span class="hljs-built_in">exp</span> <span class="hljs-operator">=</span> vsted<span class="hljs-punctuation">,</span> expSample <span class="hljs-operator">=</span> incSample<span class="hljs-punctuation">,</span> R <span class="hljs-operator">=</span> <span class="hljs-number">200</span><span class="hljs-punctuation">,</span><br>           nCategory <span class="hljs-operator">=</span> <span class="hljs-number">5</span><span class="hljs-punctuation">,</span><br>           compareRef<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> <br>           expRow<span class="hljs-operator">=</span><span class="hljs-string">&#x27;ENSEMBL&#x27;</span><span class="hljs-punctuation">,</span> orgDb<span class="hljs-operator">=</span>org.Hs.eg.db<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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