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  133. <h1 id="seo-header">regplot绘制高级nomogram</h1>
  134. <div class="markdown-body">
  135. <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>
  136. <li><a target="_blank" rel="noopener" href="https://occdn.limour.top/2215.html">conda activate ggsurvplot</a></li>
  137. <li>install.packages(‘regplot’)</li>
  138. </ul>
  139. <h2 id="高级nomogram"><a href="#高级nomogram" class="headerlink" title="高级nomogram"></a>高级nomogram</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></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><span class="hljs-string">&quot;survival&quot;</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;survminer&quot;</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>regplot<span class="hljs-punctuation">)</span><br>mycol<span class="hljs-operator">&lt;-</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;#A6CEE3&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#1F78B4&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#33adff&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#2166AC&quot;</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>mycol<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-string">&quot;dencol&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;boxcocl&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;obscol&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;spkcol&quot;</span><span class="hljs-punctuation">)</span><br>mycol<span class="hljs-operator">&lt;-</span> as.list<span class="hljs-punctuation">(</span>mycol<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">8</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>f1 <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>
  140. <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">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">12</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#123;</span>pdf<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;nomogram_new.pdf&quot;</span><span class="hljs-punctuation">)</span>;<span class="hljs-punctuation">&#123;</span><br>print<span class="hljs-punctuation">(</span>dev.list<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> dev.set<span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><br> regplot<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span><br><span class="hljs-comment"># observation=df[1,], #也可以不展示</span><br> failtime <span class="hljs-operator">=</span> <span class="hljs-number">12</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-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">,</span><span class="hljs-number">5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#预测1年、3年和5年的死亡风险</span><br> prfail <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#cox回归中需要TRUE</span><br> showP <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#是否展示统计学差异</span><br> droplines <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#观测2示例计分是否画线</span><br> colors <span class="hljs-operator">=</span> mycol<span class="hljs-punctuation">,</span> <span class="hljs-comment">#用前面自己定义的颜色</span><br> interval<span class="hljs-operator">=</span><span class="hljs-string">&quot;confidence&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">#展示观测的可信区间</span><br> clickable<span class="hljs-operator">=</span><span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span> <br>print<span class="hljs-punctuation">(</span>dev.list<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>graphics.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  141. <p>博主PS:这个regplot的绘图输出好奇怪,不知道为啥这样写可以被pdf捕获</p>
  142. <h2 id="重抽样校正曲线"><a href="#重抽样校正曲线" class="headerlink" title="重抽样校正曲线"></a>重抽样校正曲线</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></pre></td><td class="code"><pre><code class="hljs R">set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>cal_0 <span class="hljs-operator">&lt;-</span> calibrate<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span> u<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> cmethod<span class="hljs-operator">=</span><span class="hljs-string">&#x27;KM&#x27;</span><span class="hljs-punctuation">,</span> method<span class="hljs-operator">=</span><span class="hljs-string">&#x27;boot&#x27;</span><span class="hljs-punctuation">,</span> m<span class="hljs-operator">=</span><span class="hljs-number">98</span><span class="hljs-punctuation">,</span> B<span class="hljs-operator">=</span><span class="hljs-number">1000</span><span class="hljs-punctuation">)</span><br>set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>cal_1 <span class="hljs-operator">&lt;-</span> calibrate<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span> u<span class="hljs-operator">=</span><span class="hljs-number">3</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> cmethod<span class="hljs-operator">=</span><span class="hljs-string">&#x27;KM&#x27;</span><span class="hljs-punctuation">,</span> method<span class="hljs-operator">=</span><span class="hljs-string">&#x27;boot&#x27;</span><span class="hljs-punctuation">,</span> m<span class="hljs-operator">=</span><span class="hljs-number">98</span><span class="hljs-punctuation">,</span> B<span class="hljs-operator">=</span><span class="hljs-number">1000</span><span class="hljs-punctuation">)</span><br>set.seed<span class="hljs-punctuation">(</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span><br>cal_2 <span class="hljs-operator">&lt;-</span> calibrate<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span> u<span class="hljs-operator">=</span><span class="hljs-number">5</span><span class="hljs-operator">*</span><span class="hljs-number">12</span><span class="hljs-punctuation">,</span> cmethod<span class="hljs-operator">=</span><span class="hljs-string">&#x27;KM&#x27;</span><span class="hljs-punctuation">,</span> method<span class="hljs-operator">=</span><span class="hljs-string">&#x27;boot&#x27;</span><span class="hljs-punctuation">,</span> m<span class="hljs-operator">=</span><span class="hljs-number">98</span><span class="hljs-punctuation">,</span> B<span class="hljs-operator">=</span><span class="hljs-number">1000</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  143. <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></pre></td><td class="code"><pre><code class="hljs R">pdf<span class="hljs-punctuation">(</span>file <span class="hljs-operator">=</span> <span class="hljs-string">&#x27;calibrate.pdf&#x27;</span><span class="hljs-punctuation">,</span> width <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">,</span> height <span class="hljs-operator">=</span> <span class="hljs-number">6</span><span class="hljs-punctuation">)</span>;<span class="hljs-punctuation">&#123;</span>plot<span class="hljs-punctuation">(</span>cal_0<span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##设置线条宽度和线条类型</span><br> errbar.col<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#0072B5AA&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##设置一个颜色</span><br> xlab<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Nomogram-Predicted Probability of DFS&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#便签</span><br> ylab<span class="hljs-operator">=</span><span class="hljs-string">&#x27;Actual DFS(proportion)&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#标签</span><br> col<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#BC3C29AA&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#设置一个颜色</span><br> xlim <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">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>ylim <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">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-comment">##x轴和y轴范围</span><br> mgp <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>plot<span class="hljs-punctuation">(</span>cal_1<span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##设置线条宽度和线条类型</span><br> errbar.col<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#20854EAA&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##设置一个颜色</span><br> col<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#E18727AA&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#设置一个颜色</span><br> add <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br> xlim <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">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>ylim <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">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-comment">##x轴和y轴范围</span><br> mgp <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-comment">#控制坐标轴的位置</span><br>plot<span class="hljs-punctuation">(</span>cal_2<span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##设置线条宽度和线条类型</span><br> errbar.col<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#6F99ADAA&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-comment">##设置一个颜色</span><br> col<span class="hljs-operator">=</span><span class="hljs-string">&#x27;#EE4C97AA&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-comment">#设置一个颜色</span><br> add <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">,</span><br> xlim <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">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>ylim <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">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-comment">##x轴和y轴范围</span><br> mgp <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span> <span class="hljs-number">1</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br>legend<span class="hljs-punctuation">(</span><span class="hljs-string">&quot;bottomleft&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;1-year&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;3-year&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;5-year&#x27;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> col<span class="hljs-operator">=</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;#BC3C29AA&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#E18727AA&quot;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&quot;#EE4C97AA&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span>lty<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span>lwd<span class="hljs-operator">=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#125;</span>;dev.off<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  144. <h2 id="导出nomogram的风险预测值"><a href="#导出nomogram的风险预测值" class="headerlink" title="导出nomogram的风险预测值"></a>导出nomogram的风险预测值</h2><figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br></pre></td><td class="code"><pre><code class="hljs R">df<span class="hljs-operator">$</span>Risk_Score <span class="hljs-operator">&lt;-</span> predict<span class="hljs-punctuation">(</span>f1<span class="hljs-punctuation">,</span>type<span class="hljs-operator">=</span><span class="hljs-string">&quot;lp&quot;</span><span class="hljs-punctuation">,</span>newdata<span class="hljs-operator">=</span>df<span class="hljs-punctuation">)</span><br>df<br></code></pre></td></tr></table></figure>
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  347. <script>Fluid.plugins.codeWidget();</script>
  348. <script>
  349. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  350. window.anchors.options = {
  351. placement: CONFIG.anchorjs.placement,
  352. visible : CONFIG.anchorjs.visible
  353. };
  354. if (CONFIG.anchorjs.icon) {
  355. window.anchors.options.icon = CONFIG.anchorjs.icon;
  356. }
  357. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  358. var res = [];
  359. for (var item of el) {
  360. res.push('.markdown-body > ' + item.trim());
  361. }
  362. if (CONFIG.anchorjs.placement === 'left') {
  363. window.anchors.options.class = 'anchorjs-link-left';
  364. }
  365. window.anchors.add(res.join(', '));
  366. Fluid.events.registerRefreshCallback(function() {
  367. if ('anchors' in window) {
  368. anchors.removeAll();
  369. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  370. var res = [];
  371. for (var item of el) {
  372. res.push('.markdown-body > ' + item.trim());
  373. }
  374. if (CONFIG.anchorjs.placement === 'left') {
  375. anchors.options.class = 'anchorjs-link-left';
  376. }
  377. anchors.add(res.join(', '));
  378. }
  379. });
  380. });
  381. </script>
  382. <script>
  383. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  384. Fluid.plugins.fancyBox();
  385. });
  386. </script>
  387. <script>Fluid.plugins.imageCaption();</script>
  388. <script src="/js/local-search.js" ></script>
  389. <!-- 主题的启动项,将它保持在最底部 -->
  390. <!-- the boot of the theme, keep it at the bottom -->
  391. <script src="/js/boot.js" ></script>
  392. <noscript>
  393. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  394. </noscript>
  395. <!-- hexo injector body_end start -->
  396. <script defer src="/theme-inject/timeliness.js"></script>
  397. <!-- hexo injector body_end end --></body>
  398. </html>