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            <h1 id="seo-header">COXPH可视化</h1>
            
            
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                <h2 id="建模"><a href="#建模" class="headerlink" title="建模"></a>建模</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">library<span class="hljs-punctuation">(</span>rms<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>survival<span class="hljs-punctuation">)</span><br>dat <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../../../COXPH/data/PRAD.rds&#x27;</span><span class="hljs-punctuation">)</span><br>pfg <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;../A_ref_A_fiig.3_A_B/pfg.rds&#x27;</span><span class="hljs-punctuation">)</span><br>y <span class="hljs-operator">&lt;-</span> Surv<span class="hljs-punctuation">(</span><span class="hljs-built_in">round</span><span class="hljs-punctuation">(</span>dat<span class="hljs-operator">$</span>meta<span class="hljs-operator">$</span>pfs_time<span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> dat<span class="hljs-operator">$</span>meta<span class="hljs-operator">$</span>pfs_status <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><br>y <span class="hljs-operator">&lt;-</span> data.matrix<span class="hljs-punctuation">(</span>y<span class="hljs-punctuation">)</span><br>x <span class="hljs-operator">&lt;-</span> dat<span class="hljs-operator">$</span>data<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span>pfg<span class="hljs-punctuation">]</span><br>x <span class="hljs-operator">&lt;-</span> as.matrix<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> cbind<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span>y<span class="hljs-punctuation">)</span><br>df <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><br>dd<span class="hljs-operator">=</span>datadist<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>datadist<span class="hljs-operator">=</span><span class="hljs-string">&quot;dd&quot;</span><span class="hljs-punctuation">)</span> <br>coxmf <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;Surv(time, status==1)~&quot;</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>df<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">5</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;+&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>coxmf<br>f2 <span class="hljs-operator">&lt;-</span> cph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data<span class="hljs-operator">=</span>df<span class="hljs-punctuation">,</span> x<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> y<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> surv <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建COX比例风险模型</span><br></code></pre></td></tr></table></figure>

<h2 id="Nomo图展示回归系数"><a href="#Nomo图展示回归系数" class="headerlink" title="Nomo图展示回归系数"></a>Nomo图展示回归系数</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></pre></td><td class="code"><pre><code class="hljs R">surv <span class="hljs-operator">&lt;-</span> Survival<span class="hljs-punctuation">(</span>f2<span class="hljs-punctuation">)</span> <span class="hljs-comment"># 构建生存概率函数</span><br>nom <span class="hljs-operator">&lt;-</span> nomogram<span class="hljs-punctuation">(</span>f2<span class="hljs-punctuation">,</span> fun<span class="hljs-operator">=</span><span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> surv<span class="hljs-punctuation">(</span><span class="hljs-number">5</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                            <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span> surv<span class="hljs-punctuation">(</span><span class="hljs-number">10</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                             funlabel<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;5-year Disease-free Probability&quot;</span><span class="hljs-punctuation">,</span><br>                                        <span class="hljs-string">&quot;10-year Disease-free Probability&quot;</span><span class="hljs-punctuation">)</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">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>plot<span class="hljs-punctuation">(</span>nom<span class="hljs-punctuation">,</span> xfrac<span class="hljs-operator">=</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span><br>pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;nomo.pdf&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">12</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">)</span>;plot<span class="hljs-punctuation">(</span>nom<span class="hljs-punctuation">,</span> xfrac<span class="hljs-operator">=</span><span class="hljs-number">.2</span><span class="hljs-punctuation">)</span>;dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>

<h2 id="森林图展示风险比"><a href="#森林图展示风险比" class="headerlink" title="森林图展示风险比"></a>森林图展示风险比</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></pre></td><td class="code"><pre><code class="hljs R">res.cox <span class="hljs-operator">&lt;-</span> coxph<span class="hljs-punctuation">(</span>formula<span class="hljs-punctuation">(</span>coxmf<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> data <span class="hljs-operator">=</span>  df<span class="hljs-punctuation">)</span><br>tmp_res <span class="hljs-operator">&lt;-</span> summary<span class="hljs-punctuation">(</span>res.cox<span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> as.data.frame<span class="hljs-punctuation">(</span>tmp_res<span class="hljs-operator">$</span>conf.int<span class="hljs-punctuation">)</span><br>res <span class="hljs-operator">&lt;-</span> res<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">4</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>colnames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;mean&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;lower&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;upper&#x27;</span><span class="hljs-punctuation">)</span><br>res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Pvalue&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp_res<span class="hljs-operator">$</span>coefficients<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;Pr(&gt;z)&#x27;</span><span class="hljs-punctuation">]</span><br>res<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;VarName&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><br>res<br>saveRDS<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;res.rds&#x27;</span><span class="hljs-punctuation">)</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><span class="line">34</span><br><span class="line">35</span><br><span class="line">36</span><br></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>forestplot<span class="hljs-punctuation">)</span><br>f_forestplot <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">,</span> xlab<span class="hljs-operator">=</span><span class="hljs-string">&quot;XR&quot;</span><span class="hljs-punctuation">,</span> zero<span class="hljs-operator">=</span><span class="hljs-number">0</span><span class="hljs-punctuation">,</span> lineheight<span class="hljs-operator">=</span>unit<span class="hljs-punctuation">(</span><span class="hljs-number">10</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;mm&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> colgap<span class="hljs-operator">=</span>unit<span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;mm&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> graphwidth<span class="hljs-operator">=</span>unit<span class="hljs-punctuation">(</span><span class="hljs-number">60</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;mm&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> title<span class="hljs-operator">=</span><span class="hljs-string">&quot;Forestplot&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br>    df_labeltext <span class="hljs-operator">&lt;-</span> df<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;VarName&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;Pvalue&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>    df_labeltext<span class="hljs-punctuation">[[</span>paste0<span class="hljs-punctuation">(</span>xlab<span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;(95%CI)&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> paste0<span class="hljs-punctuation">(</span>sprintf<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;%0.2f&quot;</span><span class="hljs-punctuation">,</span> df<span class="hljs-operator">$</span>mean<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;(&#x27;</span><span class="hljs-punctuation">,</span>sprintf<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;%0.2f&quot;</span><span class="hljs-punctuation">,</span> df<span class="hljs-operator">$</span>lower<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;~&#x27;</span><span class="hljs-punctuation">,</span>sprintf<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;%0.2f&quot;</span><span class="hljs-punctuation">,</span> df<span class="hljs-operator">$</span>upper<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;)&#x27;</span><span class="hljs-punctuation">)</span><br>    df_labeltext<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Pvalue&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> sprintf<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;%0.1e&#x27;</span><span class="hljs-punctuation">,</span> df_labeltext<span class="hljs-punctuation">[[</span><span class="hljs-string">&#x27;Pvalue&#x27;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br>    df_labeltext <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span>colnames<span class="hljs-punctuation">(</span>df_labeltext<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> df_labeltext<span class="hljs-punctuation">)</span><br>    df <span class="hljs-operator">&lt;-</span> rbind<span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NaN</span><span class="hljs-punctuation">,</span> ncol<span class="hljs-punctuation">(</span>df<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> df<span class="hljs-punctuation">)</span><br>    forestplot<span class="hljs-punctuation">(</span>labeltext<span class="hljs-operator">=</span>as.matrix<span class="hljs-punctuation">(</span>df_labeltext<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-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>               mean<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>mean<span class="hljs-punctuation">,</span><br>               lower<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>lower<span class="hljs-punctuation">,</span><br>               upper<span class="hljs-operator">=</span>df<span class="hljs-operator">$</span>upper<span class="hljs-punctuation">,</span><br>               zero<span class="hljs-operator">=</span>zero<span class="hljs-punctuation">,</span><br>               boxsize<span class="hljs-operator">=</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span><br>               lineheight<span class="hljs-operator">=</span>lineheight<span class="hljs-punctuation">,</span><br>               colgap<span class="hljs-operator">=</span>colgap<span class="hljs-punctuation">,</span><br>               graphwidth<span class="hljs-operator">=</span>graphwidth<span class="hljs-punctuation">,</span><br>               lwd.zero<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><br>               lwd.ci<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <br>               col<span class="hljs-operator">=</span>fpColors<span class="hljs-punctuation">(</span>box<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#458B00&#x27;</span><span class="hljs-punctuation">,</span><br>                            summary<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#8B008B&#x27;</span><span class="hljs-punctuation">,</span><br>                            lines <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;black&#x27;</span><span class="hljs-punctuation">,</span><br>                            zero <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;#7AC5CD&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>               xlab<span class="hljs-operator">=</span>xlab<span class="hljs-punctuation">,</span><br>               lwd.xaxis <span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><br>               txt_gp <span class="hljs-operator">=</span> fpTxtGp<span class="hljs-punctuation">(</span>ticks <span class="hljs-operator">=</span> gpar<span class="hljs-punctuation">(</span>cex <span class="hljs-operator">=</span> <span class="hljs-number">0.85</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                                xlab  <span class="hljs-operator">=</span> gpar<span class="hljs-punctuation">(</span>cex <span class="hljs-operator">=</span> <span class="hljs-number">0.8</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>                                cex <span class="hljs-operator">=</span> <span class="hljs-number">0.9</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br>               lty.ci<span class="hljs-operator">=</span><span class="hljs-string">&quot;solid&quot;</span><span class="hljs-punctuation">,</span><br>               title<span class="hljs-operator">=</span>title<span class="hljs-punctuation">,</span> <br>               line.margin <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span><br>               graph.pos<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br>res <span class="hljs-operator">&lt;-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;res.rds&#x27;</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">4</span><span class="hljs-punctuation">)</span><br>p <span class="hljs-operator">&lt;-</span> f_forestplot<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> zero <span class="hljs-operator">=</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> xlab <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;HR&#x27;</span><span class="hljs-punctuation">)</span><br>p<br></code></pre></td></tr></table></figure>
                
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        var res = [];
        for (var item of el) {
          res.push('.markdown-body > ' + item.trim());
        }
        if (CONFIG.anchorjs.placement === 'left') {
          anchors.options.class = 'anchorjs-link-left';
        }
        anchors.add(res.join(', '));
      }
    });
  });
</script>


<script>
  Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
    Fluid.plugins.fancyBox();
  });
</script>


  <script>Fluid.plugins.imageCaption();</script>

  <script  src="/js/local-search.js" ></script>


<!-- 主题的启动项，将它保持在最底部 -->
<!-- the boot of the theme, keep it at the bottom -->
<script  src="/js/boot.js" ></script>


  <noscript>
    <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  </noscript>
<!-- hexo injector body_end start -->
  <script defer src="/theme-inject/timeliness.js"></script>
<!-- hexo injector body_end end --></body>
</html>