2225.html 44 KB

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638
  1. <!DOCTYPE html>
  2. <html lang="en" data-default-color-scheme=auto>
  3. <head><!-- hexo injector head_begin start -->
  4. <script async src="https://analytics.umami.is/script.js" data-website-id="e59ec28a-c9a7-4104-9e62-a9f7eb3fac0b"></script>
  5. <!-- hexo injector head_begin end -->
  6. <meta charset="UTF-8">
  7. <link rel="apple-touch-icon" sizes="76x76" href="https://img.limour.top/2023/08/29/64ee07361815a.webp">
  8. <link rel="icon" href="https://img.limour.top/2023/08/29/64ee07361815a.webp">
  9. <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=5.0, shrink-to-fit=no">
  10. <meta http-equiv="x-ua-compatible" content="ie=edge">
  11. <meta name="theme-color" content="#2f4154">
  12. <meta name="author" content="Limour">
  13. <meta name="keywords" content="">
  14. <meta name="description" content="安装补充包 conda activate ggsurvplot # conda install -c conda-forge r-ggplotify -y conda install -c conda-forge r-circlize -y conda install -c bioconda bioconductor-complexheatmap -y install.packages(‘ggri">
  15. <meta property="og:type" content="article">
  16. <meta property="og:title" content="COX模型可视化:风险得分关联图">
  17. <meta property="og:url" content="https://occdn.limour.top/2225.html">
  18. <meta property="og:site_name" content="Limour&#39;s Blog">
  19. <meta property="og:description" content="安装补充包 conda activate ggsurvplot # conda install -c conda-forge r-ggplotify -y conda install -c conda-forge r-circlize -y conda install -c bioconda bioconductor-complexheatmap -y install.packages(‘ggri">
  20. <meta property="og:locale" content="en_US">
  21. <meta property="article:published_time" content="2022-08-11T12:30:55.000Z">
  22. <meta property="article:modified_time" content="2023-09-01T13:28:03.369Z">
  23. <meta property="article:author" content="Limour">
  24. <meta name="twitter:card" content="summary_large_image">
  25. <title>COX模型可视化:风险得分关联图 - Limour&#39;s Blog</title>
  26. <link rel="stylesheet" href="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/css/bootstrap.min.css" />
  27. <link rel="stylesheet" href="https://jscdn.limour.top/npm/github-markdown-css@4.0.0/github-markdown.min.css" />
  28. <link rel="stylesheet" href="https://jscdn.limour.top/npm/hint.css@2.7.0/hint.min.css" />
  29. <link rel="stylesheet" href="https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.css" />
  30. <!-- 主题依赖的图标库,不要自行修改 -->
  31. <!-- Do not modify the link that theme dependent icons -->
  32. <link rel="stylesheet" href="//at.alicdn.com/t/font_1749284_hj8rtnfg7um.css">
  33. <link rel="stylesheet" href="//at.alicdn.com/t/font_1736178_lbnruvf0jn.css">
  34. <link rel="stylesheet" href="/css/main.css" />
  35. <link id="highlight-css" rel="stylesheet" href="/css/highlight.css" />
  36. <link id="highlight-css-dark" rel="stylesheet" href="/css/highlight-dark.css" />
  37. <link rel="stylesheet" href="/theme-inject/custom.css">
  38. <script id="fluid-configs">
  39. var Fluid = window.Fluid || {};
  40. Fluid.ctx = Object.assign({}, Fluid.ctx)
  41. var CONFIG = {"hostname":"occdn.limour.top","root":"/","version":"1.9.5-a","typing":{"enable":true,"typeSpeed":70,"cursorChar":"_","loop":false,"scope":[]},"anchorjs":{"enable":true,"element":"h1,h2,h3,h4,h5,h6","placement":"left","visible":"hover","icon":"§"},"progressbar":{"enable":true,"height_px":3,"color":"#29d","options":{"showSpinner":false,"trickleSpeed":100}},"code_language":{"enable":true,"default":"TEXT"},"copy_btn":true,"image_caption":{"enable":true},"image_zoom":{"enable":true,"img_url_replace":["",""]},"toc":{"enable":true,"placement":"right","headingSelector":"h1,h2,h3,h4,h5,h6","collapseDepth":0},"lazyload":{"enable":true,"loading_img":"https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg","onlypost":false,"offset_factor":2},"web_analytics":{"enable":false,"follow_dnt":true,"baidu":null,"google":{"measurement_id":null},"tencent":{"sid":null,"cid":null},"woyaola":null,"cnzz":null,"leancloud":{"app_id":null,"app_key":null,"server_url":null,"path":"window.location.pathname","ignore_local":false}},"search_path":"/local-search.xml","include_content_in_search":true};
  42. if (CONFIG.web_analytics.follow_dnt) {
  43. var dntVal = navigator.doNotTrack || window.doNotTrack || navigator.msDoNotTrack;
  44. Fluid.ctx.dnt = dntVal && (dntVal.startsWith('1') || dntVal.startsWith('yes') || dntVal.startsWith('on'));
  45. }
  46. </script>
  47. <script src="/js/utils.js" ></script>
  48. <script src="/js/color-schema.js" ></script>
  49. <meta name="generator" content="Hexo 6.3.0"></head>
  50. <body>
  51. <header>
  52. <div class="header-inner" style="height: 70vh;">
  53. <nav id="navbar" class="navbar fixed-top navbar-expand-lg navbar-dark scrolling-navbar">
  54. <div class="container">
  55. <a class="navbar-brand" href="/">
  56. <strong>Limour&#39;s Blog</strong>
  57. </a>
  58. <button id="navbar-toggler-btn" class="navbar-toggler" type="button" data-toggle="collapse"
  59. data-target="#navbarSupportedContent"
  60. aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
  61. <div class="animated-icon"><span></span><span></span><span></span></div>
  62. </button>
  63. <!-- Collapsible content -->
  64. <div class="collapse navbar-collapse" id="navbarSupportedContent">
  65. <ul class="navbar-nav ml-auto text-center">
  66. <li class="nav-item">
  67. <a class="nav-link" href="/">
  68. <i class="iconfont icon-home-fill"></i>
  69. <span>Home</span>
  70. </a>
  71. </li>
  72. <li class="nav-item">
  73. <a class="nav-link" href="/archives/">
  74. <i class="iconfont icon-archive-fill"></i>
  75. <span>Archives</span>
  76. </a>
  77. </li>
  78. <li class="nav-item" id="search-btn">
  79. <a class="nav-link" target="_self" href="javascript:;" data-toggle="modal" data-target="#modalSearch" aria-label="Search">
  80. <i class="iconfont icon-search"></i>
  81. </a>
  82. </li>
  83. <li class="nav-item" id="color-toggle-btn">
  84. <a class="nav-link" target="_self" href="javascript:;" aria-label="Color Toggle">
  85. <i class="iconfont icon-dark" id="color-toggle-icon"></i>
  86. </a>
  87. </li>
  88. </ul>
  89. </div>
  90. </div>
  91. </nav>
  92. <div id="banner" class="banner" parallax=true
  93. style="background: url('https://img.limour.top/2023/08/29/64ee08e108638.webp') no-repeat center center; background-size: cover;">
  94. <div class="full-bg-img">
  95. <div class="mask flex-center" style="background-color: rgba(0, 0, 0, 0.3)">
  96. <div class="banner-text text-center fade-in-up">
  97. <div class="h2">
  98. <span id="subtitle" data-typed-text="COX模型可视化:风险得分关联图"></span>
  99. </div>
  100. <div class="mt-3">
  101. <span class="post-meta">
  102. <i class="iconfont icon-date-fill" aria-hidden="true"></i>
  103. <time datetime="2022-08-11 20:30" pubdate>
  104. August 11, 2022 pm
  105. </time>
  106. </span>
  107. </div>
  108. <div class="mt-1">
  109. <span class="post-meta mr-2">
  110. <i class="iconfont icon-chart"></i>
  111. 3.5k words
  112. </span>
  113. <span class="post-meta mr-2">
  114. <i class="iconfont icon-clock-fill"></i>
  115. 30 mins
  116. </span>
  117. </div>
  118. </div>
  119. </div>
  120. </div>
  121. </div>
  122. </div>
  123. </header>
  124. <main>
  125. <div class="container-fluid nopadding-x">
  126. <div class="row nomargin-x">
  127. <div class="side-col d-none d-lg-block col-lg-2">
  128. </div>
  129. <div class="col-lg-8 nopadding-x-md">
  130. <div class="container nopadding-x-md" id="board-ctn">
  131. <div id="board">
  132. <article class="post-content mx-auto">
  133. <h1 id="seo-header">COX模型可视化:风险得分关联图</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 href="https://occdn.limour.top/2223.html">conda activate ggsurvplot</a></li>
  137. <li># conda install -c conda-forge r-ggplotify -y</li>
  138. <li>conda install -c conda-forge r-circlize -y</li>
  139. <li>conda install -c bioconda bioconductor-complexheatmap -y</li>
  140. <li>install.packages(‘ggrisk’)</li>
  141. </ul>
  142. <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>
  143. <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">$</span>RMST<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;RMST (arm=1)&#x27;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&#x27;RMST (arm=0)&#x27;</span><span class="hljs-punctuation">)</span><br> res<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  144. <figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br></pre></td><td class="code"><pre><code class="hljs R">df<span class="hljs-operator">$</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>
  145. <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>
  146. <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>
  147. <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>
  148. </div>
  149. <hr/>
  150. <div>
  151. <div class="post-metas my-3">
  152. <div class="post-meta mr-3 d-flex align-items-center">
  153. <i class="iconfont icon-category"></i>
  154. <span class="category-chains">
  155. <span class="category-chain">
  156. <a href="/categories/%E7%BB%98%E5%9B%BE/" class="category-chain-item">绘图</a>
  157. </span>
  158. </span>
  159. </div>
  160. </div>
  161. <div class="license-box my-3">
  162. <div class="license-title">
  163. <div>COX模型可视化:风险得分关联图</div>
  164. <div>https://occdn.limour.top/2225.html</div>
  165. </div>
  166. <div class="license-meta">
  167. <div class="license-meta-item">
  168. <div>Author</div>
  169. <div>Limour</div>
  170. </div>
  171. <div class="license-meta-item license-meta-date">
  172. <div>Posted on</div>
  173. <div>August 11, 2022</div>
  174. </div>
  175. <div class="license-meta-item">
  176. <div>Licensed under</div>
  177. <div>
  178. <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
  179. <span class="hint--top hint--rounded" aria-label="BY - Attribution">
  180. <i class="iconfont icon-by"></i>
  181. </span>
  182. </a>
  183. <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
  184. <span class="hint--top hint--rounded" aria-label="NC - Non-commercial">
  185. <i class="iconfont icon-nc"></i>
  186. </span>
  187. </a>
  188. <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
  189. <span class="hint--top hint--rounded" aria-label="SA - Share-alike">
  190. <i class="iconfont icon-sa"></i>
  191. </span>
  192. </a>
  193. </div>
  194. </div>
  195. </div>
  196. <div class="license-icon iconfont"></div>
  197. </div>
  198. <div class="post-prevnext my-3">
  199. <article class="post-prev col-6">
  200. <a href="/2228.html" title="Rstudio-server:安装seurat">
  201. <i class="iconfont icon-arrowleft"></i>
  202. <span class="hidden-mobile">Rstudio-server:安装seurat</span>
  203. <span class="visible-mobile">Previous</span>
  204. </a>
  205. </article>
  206. <article class="post-next col-6">
  207. <a href="/2223.html" title="regplot绘制高级nomogram">
  208. <span class="hidden-mobile">regplot绘制高级nomogram</span>
  209. <span class="visible-mobile">Next</span>
  210. <i class="iconfont icon-arrowright"></i>
  211. </a>
  212. </article>
  213. </div>
  214. </div>
  215. </article>
  216. </div>
  217. </div>
  218. </div>
  219. <div class="side-col d-none d-lg-block col-lg-2">
  220. <aside class="sidebar" style="margin-left: -1rem">
  221. <div id="toc">
  222. <p class="toc-header">
  223. <i class="iconfont icon-list"></i>
  224. <span>Table of Contents</span>
  225. </p>
  226. <div class="toc-body" id="toc-body"></div>
  227. </div>
  228. </aside>
  229. </div>
  230. </div>
  231. </div>
  232. <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
  233. <i class="iconfont icon-arrowup" aria-hidden="true"></i>
  234. </a>
  235. <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
  236. aria-hidden="true">
  237. <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
  238. <div class="modal-content">
  239. <div class="modal-header text-center">
  240. <h4 class="modal-title w-100 font-weight-bold">Search</h4>
  241. <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
  242. <span aria-hidden="true">&times;</span>
  243. </button>
  244. </div>
  245. <div class="modal-body mx-3">
  246. <div class="md-form mb-5">
  247. <input type="text" id="local-search-input" class="form-control validate">
  248. <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
  249. </div>
  250. <div class="list-group" id="local-search-result"></div>
  251. </div>
  252. </div>
  253. </div>
  254. </div>
  255. </main>
  256. <footer>
  257. <div class="footer-inner">
  258. <div class="footer-content">
  259. <a target="_blank" rel="nofollow noopener" href="http://www.beian.gov.cn/portal/registerSystemInfo?recordcode=43130202000203"><img src="https://img.limour.top/2023/08/27/64eadeb81d6a0.webp" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload>湘公网安备 43130202000203号 </a> <a target="_blank" rel="nofollow noopener" href="https://beian.miit.gov.cn/">湘ICP备20008299号 </a> <a target="_blank" rel="nofollow noopener" href="https://icp.gov.moe/?keyword=20210128">萌ICP备20210128号</a> <br> <a href="https://www.foreverblog.cn/" target="_blank"> <img src="https://img.foreverblog.cn/logo_en_default.png" srcset="https://jscdn.limour.top/gh/Limour-dev/Sakurairo_Vision/load_svg/inload.svg" lazyload alt="" style="width:auto;height:24px"> </a> <br> <a href="https://hexo.io" target="_blank" rel="nofollow noopener"><span>Hexo</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/fluid-dev/hexo-theme-fluid" target="_blank" rel="nofollow noopener"><span>Fluid</span></a> <i class="iconfont icon-love"></i> <a href="https://github.com/limour-blog/archives-occdn" target="_blank" rel="nofollow noopener"><span>SRC</span></a>
  260. </div>
  261. </div>
  262. </footer>
  263. <!-- Scripts -->
  264. <script src="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.js" ></script>
  265. <link rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />
  266. <script>
  267. NProgress.configure({"showSpinner":false,"trickleSpeed":100})
  268. NProgress.start()
  269. window.addEventListener('load', function() {
  270. NProgress.done();
  271. })
  272. </script>
  273. <script src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
  274. <script src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
  275. <script src="/js/events.js" ></script>
  276. <script src="/js/plugins.js" ></script>
  277. <script src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  278. <script>
  279. (function (window, document) {
  280. var typing = Fluid.plugins.typing;
  281. var subtitle = document.getElementById('subtitle');
  282. if (!subtitle || !typing) {
  283. return;
  284. }
  285. var text = subtitle.getAttribute('data-typed-text');
  286. typing(text);
  287. })(window, document);
  288. </script>
  289. <script src="/js/img-lazyload.js" ></script>
  290. <script>
  291. Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
  292. var toc = jQuery('#toc');
  293. if (toc.length === 0 || !window.tocbot) { return; }
  294. var boardCtn = jQuery('#board-ctn');
  295. var boardTop = boardCtn.offset().top;
  296. window.tocbot.init(Object.assign({
  297. tocSelector : '#toc-body',
  298. contentSelector : '.markdown-body',
  299. linkClass : 'tocbot-link',
  300. activeLinkClass : 'tocbot-active-link',
  301. listClass : 'tocbot-list',
  302. isCollapsedClass: 'tocbot-is-collapsed',
  303. collapsibleClass: 'tocbot-is-collapsible',
  304. scrollSmooth : true,
  305. includeTitleTags: true,
  306. headingsOffset : -boardTop,
  307. }, CONFIG.toc));
  308. if (toc.find('.toc-list-item').length > 0) {
  309. toc.css('visibility', 'visible');
  310. }
  311. Fluid.events.registerRefreshCallback(function() {
  312. if ('tocbot' in window) {
  313. tocbot.refresh();
  314. var toc = jQuery('#toc');
  315. if (toc.length === 0 || !tocbot) {
  316. return;
  317. }
  318. if (toc.find('.toc-list-item').length > 0) {
  319. toc.css('visibility', 'visible');
  320. }
  321. }
  322. });
  323. });
  324. </script>
  325. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  326. <script>Fluid.plugins.codeWidget();</script>
  327. <script>
  328. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  329. window.anchors.options = {
  330. placement: CONFIG.anchorjs.placement,
  331. visible : CONFIG.anchorjs.visible
  332. };
  333. if (CONFIG.anchorjs.icon) {
  334. window.anchors.options.icon = CONFIG.anchorjs.icon;
  335. }
  336. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  337. var res = [];
  338. for (var item of el) {
  339. res.push('.markdown-body > ' + item.trim());
  340. }
  341. if (CONFIG.anchorjs.placement === 'left') {
  342. window.anchors.options.class = 'anchorjs-link-left';
  343. }
  344. window.anchors.add(res.join(', '));
  345. Fluid.events.registerRefreshCallback(function() {
  346. if ('anchors' in window) {
  347. anchors.removeAll();
  348. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  349. var res = [];
  350. for (var item of el) {
  351. res.push('.markdown-body > ' + item.trim());
  352. }
  353. if (CONFIG.anchorjs.placement === 'left') {
  354. anchors.options.class = 'anchorjs-link-left';
  355. }
  356. anchors.add(res.join(', '));
  357. }
  358. });
  359. });
  360. </script>
  361. <script>
  362. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  363. Fluid.plugins.fancyBox();
  364. });
  365. </script>
  366. <script>Fluid.plugins.imageCaption();</script>
  367. <script src="/js/local-search.js" ></script>
  368. <!-- 主题的启动项,将它保持在最底部 -->
  369. <!-- the boot of the theme, keep it at the bottom -->
  370. <script src="/js/boot.js" ></script>
  371. <noscript>
  372. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  373. </noscript>
  374. <!-- hexo injector body_end start -->
  375. <script defer src="/theme-inject/timeliness.js"></script>
  376. <!-- hexo injector body_end end --></body>
  377. </html>