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            <h1 id="seo-header">COX模型可视化：风险得分关联图</h1>
            
            
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                <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/2223.html">conda activate ggsurvplot</a></li>
<li># conda install -c conda-forge r-ggplotify -y</li>
<li>conda install -c conda-forge r-circlize -y</li>
<li>conda install -c bioconda bioconductor-complexheatmap -y</li>
<li>install.packages(‘ggrisk’)</li>
</ul>
<h2 id="绘制风险得分关联图"><a href="#绘制风险得分关联图" class="headerlink" title="绘制风险得分关联图"></a>绘制风险得分关联图</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>ggrisk<span class="hljs-punctuation">)</span><br>ggrisk<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span><br>       code.highrisk <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;High Risk&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#高风险标签，默认为 ’High’</span><br>       code.lowrisk <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Low Risk&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#低风险标签，默认为 ’Low’</span><br>       title.A.ylab<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Risk Score&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#A图 y轴名称</span><br>       title.B.ylab<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Survival Time(month)&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#B图 y轴名称，注意区分year month day</span><br>       title.A.legend<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Risk Group&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#A图图例名称</span><br>       title.B.legend<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Status&#x27;</span><span class="hljs-punctuation">,</span>     <span class="hljs-comment">#B图图例名称</span><br>       title.C.legend<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Relative Expression&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#C图图例名称</span><br>       relative_heights<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.1</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.01</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.15</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#A、B、热图注释和热图C的相对高度    </span><br>       color.A<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>low<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#99CCFFAA&#x27;</span><span class="hljs-punctuation">,</span>high<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#FF6666AA&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#A图中点的颜色</span><br>       color.B<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>code.0<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#99CCFFAA&#x27;</span><span class="hljs-punctuation">,</span>code.1<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#FF6666AA&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#B图中点的颜色</span><br>       color.C<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>low<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#99CCFFAA&#x27;</span><span class="hljs-punctuation">,</span>median<span class="hljs-operator">=</span><span class="hljs-string">&#x27;white&#x27;</span><span class="hljs-punctuation">,</span>high<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#FF6666FF&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#C图中热图颜色</span><br>       vjust.A.ylab<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#A图中y轴标签到y坐标轴的距离,默认是1</span><br>       vjust.B.ylab<span class="hljs-operator">=</span><span class="hljs-number">2</span>  <span class="hljs-comment">#B图中y轴标签到y坐标轴的距离,默认是2</span><br>       <span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="绘制生存曲线"><a href="#绘制生存曲线" class="headerlink" title="绘制生存曲线"></a>绘制生存曲线</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">library<span class="hljs-punctuation">(</span>survival<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survminer<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggpubr<span class="hljs-punctuation">)</span><br>require<span class="hljs-punctuation">(</span>survRM2<span class="hljs-punctuation">)</span><br>f_surv <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> isplot<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> timeN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;time&#x27;</span><span class="hljs-punctuation">,</span> statusN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;status&#x27;</span><span class="hljs-punctuation">,</span> groupN<span class="hljs-operator">=</span><span class="hljs-string">&#x27;group&#x27;</span><span class="hljs-punctuation">,</span> tau<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-punctuation">,</span> risk.table<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> ncensor.plot<span class="hljs-operator">=</span><span class="hljs-built_in">T</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>    my.surv <span class="hljs-operator">&lt;&lt;-</span> Surv<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>timeN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> df<span class="hljs-punctuation">[[</span>statusN<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><br>    my.surv.f <span class="hljs-operator">&lt;&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;my.surv~&quot;</span><span class="hljs-punctuation">,</span> groupN<span class="hljs-punctuation">)</span><br>    my.surv.df <span class="hljs-operator">&lt;&lt;-</span> df<br>    kmfit <span class="hljs-operator">&lt;-</span> surv_fit<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>my.surv.f<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> my.surv.df<span class="hljs-punctuation">)</span><br>    sdiff <span class="hljs-operator">&lt;-</span> survdiff<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>my.surv.f<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span> my.surv.df<span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>pv <span class="hljs-operator">&lt;-</span> 1 <span class="hljs-operator">-</span> pchisq<span class="hljs-punctuation">(</span>sdiff<span class="hljs-operator">$</span>chisq<span class="hljs-punctuation">,</span> <span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>sdiff<span class="hljs-operator">$</span>n<span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>    <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>isplot<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>        res<span class="hljs-operator">$</span>plot <span class="hljs-operator">&lt;-</span> ggsurvplot<span class="hljs-punctuation">(</span>kmfit<span class="hljs-punctuation">,</span> conf.int <span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> pval <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> risk.table <span class="hljs-operator">=</span> risk.table<span class="hljs-punctuation">,</span> ncensor.plot <span class="hljs-operator">=</span> ncensor.plot<span class="hljs-punctuation">)</span><br>    <span class="hljs-punctuation">&#125;</span><br>    res<span class="hljs-operator">$</span>RMS <span class="hljs-operator">&lt;-</span> rmst2<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>timeN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> df<span class="hljs-punctuation">[[</span>statusN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">as.numeric</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">[[</span>groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> tau<span class="hljs-operator">=</span>tau<span class="hljs-punctuation">)</span><br>    res<span class="hljs-operator">$</span>RMST <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>rbind<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>RMS<span class="hljs-operator">$</span>RMST.arm1<span class="hljs-operator">$</span>result<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>res<span class="hljs-operator">$</span>RMS<span class="hljs-operator">$</span>RMST.arm0<span class="hljs-operator">$</span>result<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>    rownames<span class="hljs-punctuation">(</span>res<span class="hljs-operator">$</span>RMST<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;RMST (arm=1)&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;RMST (arm=0)&#x27;</span><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></pre></td><td class="code"><pre><code class="hljs R">df<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;Low Risk&#x27;</span><br>df<span class="hljs-operator">$</span>group<span class="hljs-punctuation">[</span>df<span class="hljs-operator">$</span>f1_points <span class="hljs-operator">&gt;</span> median<span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>f1_points<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-string">&#x27;High Risk&#x27;</span><br>df<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> as.factor<span class="hljs-punctuation">(</span>df<span class="hljs-operator">$</span>group<span class="hljs-punctuation">)</span><br>test <span class="hljs-operator">&lt;-</span> f_surv<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> tau <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-operator">*</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span> risk.table <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span> ncensor.plot<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>repr.plot.width<span class="hljs-operator">=</span><span class="hljs-number">6</span><span class="hljs-punctuation">,</span> repr.plot.height<span class="hljs-operator">=</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><br>test<span class="hljs-operator">$</span>plot<br></code></pre></td></tr></table></figure>

<h2 id="绘制ComplexHeatmap"><a href="#绘制ComplexHeatmap" class="headerlink" title="绘制ComplexHeatmap"></a>绘制ComplexHeatmap</h2><p>更详细的绘制见知乎答主：<a target="_blank" rel="noopener" href="https://zhuanlan.zhihu.com/p/372130351">生信学习手册</a></p>
<h3 id="准备数据"><a href="#准备数据" class="headerlink" title="准备数据"></a>准备数据</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></pre></td><td class="code"><pre><code class="hljs R">dfc <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;clinical.rds&#x27;</span><span class="hljs-punctuation">)</span><br>dfc <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>df1<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>dfc<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">11</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>dfc<span class="hljs-punctuation">)</span><br>dfc<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> df<span class="hljs-operator">$</span>group<br>results <span class="hljs-operator">&lt;-</span> formula_rd<span class="hljs-punctuation">(</span>nomogram <span class="hljs-operator">=</span> nom1<span class="hljs-punctuation">)</span><br>dfc<span class="hljs-operator">$</span>Risk_Points <span class="hljs-operator">&lt;-</span> points_cal<span class="hljs-punctuation">(</span>formula <span class="hljs-operator">=</span> results<span class="hljs-operator">$</span>formula<span class="hljs-punctuation">,</span>rd<span class="hljs-operator">=</span>dfc<span class="hljs-punctuation">)</span><br>dfc<br>saveRDS<span class="hljs-punctuation">(</span>dfc<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;dfc.rds&#x27;</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h3 id="绘图"><a href="#绘图" class="headerlink" title="绘图"></a>绘图</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><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">dfc <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;clinical.rds&#x27;</span><span class="hljs-punctuation">)</span><br>dfc <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>df1<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>dfc<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">11</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>dfc<span class="hljs-punctuation">)</span><br>dfc<span class="hljs-operator">$</span>group <span class="hljs-operator">&lt;-</span> df<span class="hljs-operator">$</span>group<br>results <span class="hljs-operator">&lt;-</span> formula_rd<span class="hljs-punctuation">(</span>nomogram <span class="hljs-operator">=</span> nom1<span class="hljs-punctuation">)</span><br>dfc<span class="hljs-operator">$</span>Risk_Points <span class="hljs-operator">&lt;-</span> points_cal<span class="hljs-punctuation">(</span>formula <span class="hljs-operator">=</span> results<span class="hljs-operator">$</span>formula<span class="hljs-punctuation">,</span>rd<span class="hljs-operator">=</span>dfc<span class="hljs-punctuation">)</span><br>dfc<br>saveRDS<span class="hljs-punctuation">(</span>dfc<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;dfc.rds&#x27;</span><span class="hljs-punctuation">)</span><br><br>library<span class="hljs-punctuation">(</span>circlize<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ComplexHeatmap<span class="hljs-punctuation">)</span><br>dfc <span class="hljs-operator">&lt;-</span> dfc<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>dfc<span class="hljs-operator">$</span>Risk_Points<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br><span class="hljs-comment">#定义注释信息</span><br>ha <span class="hljs-operator">&lt;-</span> HeatmapAnnotation<span class="hljs-punctuation">(</span>`Risk group` <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>group<span class="hljs-punctuation">,</span><br>                        `Risk Points` <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>Risk_Points<span class="hljs-punctuation">,</span><br>                        DFS.status <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>status<span class="hljs-punctuation">,</span><br>                        DFS.time <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>time<span class="hljs-punctuation">,</span><br>                        <span class="hljs-built_in">T</span> <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br>                        N <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>N<span class="hljs-punctuation">,</span><br>                        M <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>M<span class="hljs-punctuation">,</span><br>                        logPSA <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>PSA<span class="hljs-punctuation">,</span><br>                        `Gleason Score` <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>GS<span class="hljs-punctuation">,</span><br>                        Age <span class="hljs-operator">=</span> dfc<span class="hljs-operator">$</span>Age<span class="hljs-punctuation">,</span><br>                        col <span class="hljs-operator">=</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><br>                            `Risk group` <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Low Risk&quot;</span> <span class="hljs-operator">=</span> <span class="hljs-string">&quot;#99CCFFAA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;High Risk&#x27;</span> <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;#FF6666AA&#x27;</span><span class="hljs-punctuation">)</span><br>                        <span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br><span class="hljs-comment">#                         annotation_name_gp = gpar(fontsize = 14),</span><br>                        show_annotation_name <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>mat <span class="hljs-operator">&lt;-</span> as.matrix<span class="hljs-punctuation">(</span>dfc<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><br>rownames<span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-literal">NULL</span><br>mat <span class="hljs-operator">&lt;-</span> t<span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">)</span><br>col_fun <span class="hljs-operator">&lt;-</span> colorRamp2<span class="hljs-punctuation">(</span><br>  <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">4</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">,</span> <span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <br>  <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;#99CCCCAA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;white&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;#BC3C29AA&quot;</span><span class="hljs-punctuation">)</span><br>  <span class="hljs-punctuation">)</span><br>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">8</span><span class="hljs-punctuation">)</span><br>Heatmap<span class="hljs-punctuation">(</span>mat<span class="hljs-punctuation">,</span> name <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;Relative Expression&#x27;</span><span class="hljs-punctuation">,</span> top_annotation <span class="hljs-operator">=</span> ha<span class="hljs-punctuation">,</span> column_order <span class="hljs-operator">=</span> order<span class="hljs-punctuation">(</span>dfc<span class="hljs-operator">$</span>Risk_Points<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>        col<span class="hljs-operator">=</span>col_fun<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
                
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    if (CONFIG.anchorjs.icon) {
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    var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
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