2232.html 47 KB

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636
  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 seurat conda install -c bioconda r-harmony -y 读取数据1234567891011121314root_path &#x3D; &quot;.&quot;f_read10x &lt;- function(dirN, ...)&amp;#123; tp_samples &lt;- list.files(file.path(r">
  15. <meta property="og:type" content="article">
  16. <meta property="og:title" content="使用Harmony算法移除批次效应">
  17. <meta property="og:url" content="https://occdn.limour.top/2232.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 seurat conda install -c bioconda r-harmony -y 读取数据1234567891011121314root_path &#x3D; &quot;.&quot;f_read10x &lt;- function(dirN, ...)&amp;#123; tp_samples &lt;- list.files(file.path(r">
  20. <meta property="og:locale" content="en_US">
  21. <meta property="article:published_time" content="2022-08-12T16:08:41.000Z">
  22. <meta property="article:modified_time" content="2023-09-01T13:28:03.377Z">
  23. <meta property="article:author" content="Limour">
  24. <meta name="twitter:card" content="summary_large_image">
  25. <title>使用Harmony算法移除批次效应 - 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="使用Harmony算法移除批次效应"></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="2022-08-13 00:08" pubdate>
  104. August 13, 2022 am
  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">使用Harmony算法移除批次效应</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/2227.html">conda activate seurat</a></li>
  137. <li>conda install -c bioconda r-harmony -y</li>
  138. </ul>
  139. <h2 id="读取数据"><a href="#读取数据" class="headerlink" title="读取数据"></a>读取数据</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></pre></td><td class="code"><pre><code class="hljs r">root_path <span class="hljs-operator">=</span> <span class="hljs-string">&quot;.&quot;</span><br>f_read10x <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dirN<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> tp_samples <span class="hljs-operator">&lt;-</span> list.files<span class="hljs-punctuation">(</span>file.path<span class="hljs-punctuation">(</span>root_path<span class="hljs-punctuation">,</span> dirN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> tp_dir <span class="hljs-operator">&lt;-</span> file.path<span class="hljs-punctuation">(</span>root_path<span class="hljs-punctuation">,</span> dirN<span class="hljs-punctuation">,</span> tp_samples<span class="hljs-punctuation">)</span><br> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>tp_dir<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> tp_samples<br> scRNA <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>lc_ba <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>tp_dir<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> counts <span class="hljs-operator">&lt;-</span> Read10X<span class="hljs-punctuation">(</span>data.dir <span class="hljs-operator">=</span> tp_dir<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> CreateSeuratObject<span class="hljs-punctuation">(</span>counts<span class="hljs-punctuation">,</span> project <span class="hljs-operator">=</span> lc_ba<span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><br> scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> PercentageFeatureSet<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^MT-&quot;</span><span class="hljs-punctuation">)</span><br> scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-string">&quot;percent.ERCC&quot;</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> PercentageFeatureSet<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>lc_ba<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> pattern <span class="hljs-operator">=</span> <span class="hljs-string">&quot;^ERCC-&quot;</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">&#125;</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  140. <h2 id="质量控制"><a href="#质量控制" class="headerlink" title="质量控制"></a>质量控制</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></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">6</span><span class="hljs-punctuation">)</span><br>options<span class="hljs-punctuation">(</span>ggrepel.max.overlaps <span class="hljs-operator">=</span> <span class="hljs-literal">Inf</span><span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>scRNAo <span class="hljs-keyword">in</span> scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> print<span class="hljs-punctuation">(</span>VlnPlot<span class="hljs-punctuation">(</span>scRNAo<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">&quot;nFeature_RNA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;nCount_RNA&quot;</span><span class="hljs-punctuation">,</span> <span class="hljs-string">&quot;percent.mt&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> ncol <span class="hljs-operator">=</span> <span class="hljs-number">3</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> labs<span class="hljs-punctuation">(</span>title <span class="hljs-operator">=</span> scRNAo<span class="hljs-operator">@</span>project.name<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">&#125;</span><br><br>scRNA<span class="hljs-operator">$</span>APAP1 <span class="hljs-operator">&lt;-</span> subset<span class="hljs-punctuation">(</span>scRNA<span class="hljs-operator">$</span>APAP1<span class="hljs-punctuation">,</span> subset <span class="hljs-operator">=</span> nFeature_RNA <span class="hljs-operator">&gt;</span> <span class="hljs-number">200</span> <span class="hljs-operator">&amp;</span> nFeature_RNA <span class="hljs-operator">&lt;</span> <span class="hljs-number">3000</span><span class="hljs-punctuation">)</span><br><br>scRNA <span class="hljs-operator">&lt;-</span> Reduce<span class="hljs-punctuation">(</span><span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">)</span> merge<span class="hljs-punctuation">(</span>...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> scRNA<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
  141. <h2 id="预处理函数"><a href="#预处理函数" class="headerlink" title="预处理函数"></a>预处理函数</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><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">f_ScaleData_RunPCA <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> scRNA <span class="hljs-operator">&lt;-</span> FindVariableFeatures<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> selection.method <span class="hljs-operator">=</span> <span class="hljs-string">&quot;vst&quot;</span><span class="hljs-punctuation">,</span> nfeatures <span class="hljs-operator">=</span> <span class="hljs-number">2000</span><span class="hljs-punctuation">)</span><br> lc_all.genes <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><br> scRNA <span class="hljs-operator">&lt;-</span> ScaleData<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> lc_all.genes<span class="hljs-punctuation">)</span><br><br> scRNA <span class="hljs-operator">&lt;-</span> RunPCA<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> features <span class="hljs-operator">=</span> VariableFeatures<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> scRNA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> print<span class="hljs-punctuation">(</span>ElbowPlot<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> ndims <span class="hljs-operator">=</span> <span class="hljs-number">40</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br>require<span class="hljs-punctuation">(</span>harmony<span class="hljs-punctuation">)</span><br>f_RunHarmony <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> dims<span class="hljs-operator">=</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">30</span><span class="hljs-punctuation">,</span> batchN<span class="hljs-operator">=</span><span class="hljs-string">&quot;batch&quot;</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> scRNA <span class="hljs-operator">=</span> scRNA <span class="hljs-operator">%&gt;%</span> RunHarmony<span class="hljs-punctuation">(</span>batchN<span class="hljs-punctuation">,</span> plot_convergence <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">,</span> max.iter.harmony <span class="hljs-operator">=</span> <span class="hljs-number">30</span><span class="hljs-punctuation">)</span><br> scRNA <span class="hljs-operator">&lt;-</span> scRNA <span class="hljs-operator">%&gt;%</span> RunUMAP<span class="hljs-punctuation">(</span>reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;harmony&quot;</span><span class="hljs-punctuation">,</span> dims <span class="hljs-operator">=</span> dims<span class="hljs-punctuation">)</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  142. <h2 id="分群函数"><a href="#分群函数" class="headerlink" title="分群函数"></a>分群函数</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></pre></td><td class="code"><pre><code class="hljs r">f_FindNeighbors <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> resolution <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> scRNA <span class="hljs-operator">&lt;-</span> scRNA <span class="hljs-operator">%&gt;%</span> FindNeighbors<span class="hljs-punctuation">(</span>reduction <span class="hljs-operator">=</span> <span class="hljs-string">&quot;harmony&quot;</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">%&gt;%</span> FindClusters<span class="hljs-punctuation">(</span>resolution <span class="hljs-operator">=</span> resolution<span class="hljs-punctuation">)</span><br> scRNA<span class="hljs-punctuation">[[</span>paste0<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;h_resolution_&#x27;</span><span class="hljs-punctuation">,</span> resolution<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Idents<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">)</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  143. <h2 id="查看分群质量"><a href="#查看分群质量" class="headerlink" title="查看分群质量"></a>查看分群质量</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><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">f_metaG2G <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">,</span> matrixN<span class="hljs-operator">=</span><span class="hljs-built_in">F</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> alltype <span class="hljs-operator">&lt;-</span> unique<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>type <span class="hljs-keyword">in</span> alltype<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> rownames<span class="hljs-punctuation">(</span>metaG<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span>metaG<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">==</span> type<span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>matrixN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> gsub<span class="hljs-punctuation">(</span><span class="hljs-string">&#x27;-&#x27;</span><span class="hljs-punctuation">,</span><span class="hljs-string">&#x27;.&#x27;</span><span class="hljs-punctuation">,</span>res<span class="hljs-punctuation">[[</span>type<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">&#125;</span><br> <span class="hljs-punctuation">&#125;</span><br> res<br><span class="hljs-punctuation">&#125;</span><br><br>f_br_cluster_f <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> lc_filter <span class="hljs-operator">&lt;-</span> unlist<span class="hljs-punctuation">(</span>unique<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">[[</span>lc_groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> lc_filter <span class="hljs-operator">&lt;-</span> lc_filter<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>lc_filter<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> lc_filter<br><span class="hljs-punctuation">&#125;</span><br><br>f_br_cluster <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">,</span> lc_labelN<span class="hljs-punctuation">,</span> lc_prop <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> lc_g <span class="hljs-operator">&lt;-</span> f_metaG2G<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">[[</span>lc_groupN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> lc_l <span class="hljs-operator">&lt;-</span> sObject<span class="hljs-punctuation">[[</span>lc_labelN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> lc_l<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> res <span class="hljs-operator">&lt;-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> f_br_cluster_f<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">,</span> lc_labelN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>lc_prop<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>Nm <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_g<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> tmp <span class="hljs-operator">&lt;-</span> prop.table<span class="hljs-punctuation">(</span>table<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">[</span>lc_g<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> res<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">&#125;</span><br> <span class="hljs-punctuation">&#125;</span><span class="hljs-keyword">else</span><span class="hljs-punctuation">&#123;</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>Nm <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_g<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> tmp <span class="hljs-operator">&lt;-</span> table<span class="hljs-punctuation">(</span>lc_l<span class="hljs-punctuation">[</span>lc_g<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> res<span class="hljs-punctuation">[[</span>Nm<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> tmp<span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">&#125;</span><br> <span class="hljs-punctuation">&#125;</span><br> res<span class="hljs-punctuation">[</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> <span class="hljs-number">0</span><br> res<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  144. <h2 id="标注函数"><a href="#标注函数" class="headerlink" title="标注函数"></a>标注函数</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><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">f_add_annotation <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_ids<span class="hljs-punctuation">,</span>lc_metaName<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> Idents<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> sObject<span class="hljs-punctuation">[[</span>lc_metaName<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_ids<span class="hljs-punctuation">)</span> <span class="hljs-operator">&lt;-</span> levels<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span><br> sObject <span class="hljs-operator">&lt;-</span> RenameIdents<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_ids<span class="hljs-punctuation">)</span><br> sObject<span class="hljs-punctuation">[[</span>lc_metaName<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> Idents<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span><br> sObject<br><span class="hljs-punctuation">&#125;</span><br><br>f_mergeMeta_pre <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> baseMetaN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>baseMetaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br>f_mergeMeta <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">,</span> metaData<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[</span>rownames<span class="hljs-punctuation">(</span>metaData<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> <span class="hljs-built_in">as.character</span><span class="hljs-punctuation">(</span>metaData<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br>f_mergeMeta_end <span class="hljs-operator">&lt;-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">,</span> metaN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">&#123;</span><br> scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">&lt;-</span> as.factor<span class="hljs-punctuation">(</span>scRNA<span class="hljs-punctuation">[[</span>metaN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> scRNA<br><span class="hljs-punctuation">&#125;</span><br></code></pre></td></tr></table></figure>
  145. </div>
  146. <hr/>
  147. <div>
  148. <div class="post-metas my-3">
  149. <div class="post-meta mr-3 d-flex align-items-center">
  150. <i class="iconfont icon-category"></i>
  151. <span class="category-chains">
  152. <span class="category-chain">
  153. <a href="/categories/%E5%88%86%E7%BE%A4/" class="category-chain-item">分群</a>
  154. </span>
  155. </span>
  156. </div>
  157. </div>
  158. <div class="license-box my-3">
  159. <div class="license-title">
  160. <div>使用Harmony算法移除批次效应</div>
  161. <div>https://occdn.limour.top/2232.html</div>
  162. </div>
  163. <div class="license-meta">
  164. <div class="license-meta-item">
  165. <div>Author</div>
  166. <div>Limour</div>
  167. </div>
  168. <div class="license-meta-item license-meta-date">
  169. <div>Posted on</div>
  170. <div>August 13, 2022</div>
  171. </div>
  172. <div class="license-meta-item">
  173. <div>Licensed under</div>
  174. <div>
  175. <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
  176. <span class="hint--top hint--rounded" aria-label="BY - Attribution">
  177. <i class="iconfont icon-by"></i>
  178. </span>
  179. </a>
  180. <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
  181. <span class="hint--top hint--rounded" aria-label="NC - Non-commercial">
  182. <i class="iconfont icon-nc"></i>
  183. </span>
  184. </a>
  185. <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
  186. <span class="hint--top hint--rounded" aria-label="SA - Share-alike">
  187. <i class="iconfont icon-sa"></i>
  188. </span>
  189. </a>
  190. </div>
  191. </div>
  192. </div>
  193. <div class="license-icon iconfont"></div>
  194. </div>
  195. <div class="post-prevnext my-3">
  196. <article class="post-prev col-6">
  197. <a href="/2235.html" title="单细胞数据去批次效应算法比较">
  198. <i class="iconfont icon-arrowleft"></i>
  199. <span class="hidden-mobile">单细胞数据去批次效应算法比较</span>
  200. <span class="visible-mobile">Previous</span>
  201. </a>
  202. </article>
  203. <article class="post-next col-6">
  204. <a href="/2228.html" title="Rstudio-server:安装seurat">
  205. <span class="hidden-mobile">Rstudio-server:安装seurat</span>
  206. <span class="visible-mobile">Next</span>
  207. <i class="iconfont icon-arrowright"></i>
  208. </a>
  209. </article>
  210. </div>
  211. </div>
  212. </article>
  213. </div>
  214. </div>
  215. </div>
  216. <div class="side-col d-none d-lg-block col-lg-2">
  217. <aside class="sidebar" style="margin-left: -1rem">
  218. <div id="toc">
  219. <p class="toc-header">
  220. <i class="iconfont icon-list"></i>
  221. <span>Table of Contents</span>
  222. </p>
  223. <div class="toc-body" id="toc-body"></div>
  224. </div>
  225. </aside>
  226. </div>
  227. </div>
  228. </div>
  229. <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
  230. <i class="iconfont icon-arrowup" aria-hidden="true"></i>
  231. </a>
  232. <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
  233. aria-hidden="true">
  234. <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
  235. <div class="modal-content">
  236. <div class="modal-header text-center">
  237. <h4 class="modal-title w-100 font-weight-bold">Search</h4>
  238. <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
  239. <span aria-hidden="true">&times;</span>
  240. </button>
  241. </div>
  242. <div class="modal-body mx-3">
  243. <div class="md-form mb-5">
  244. <input type="text" id="local-search-input" class="form-control validate">
  245. <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
  246. </div>
  247. <div class="list-group" id="local-search-result"></div>
  248. </div>
  249. </div>
  250. </div>
  251. </div>
  252. </main>
  253. <footer>
  254. <div class="footer-inner">
  255. <div class="footer-content">
  256. <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>
  257. </div>
  258. </div>
  259. </footer>
  260. <!-- Scripts -->
  261. <script src="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.js" ></script>
  262. <link rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />
  263. <script>
  264. NProgress.configure({"showSpinner":false,"trickleSpeed":100})
  265. NProgress.start()
  266. window.addEventListener('load', function() {
  267. NProgress.done();
  268. })
  269. </script>
  270. <script src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
  271. <script src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
  272. <script src="/js/events.js" ></script>
  273. <script src="/js/plugins.js" ></script>
  274. <script src="https://lib.baomitu.com/typed.js/2.0.12/typed.min.js" ></script>
  275. <script>
  276. (function (window, document) {
  277. var typing = Fluid.plugins.typing;
  278. var subtitle = document.getElementById('subtitle');
  279. if (!subtitle || !typing) {
  280. return;
  281. }
  282. var text = subtitle.getAttribute('data-typed-text');
  283. typing(text);
  284. })(window, document);
  285. </script>
  286. <script src="/js/img-lazyload.js" ></script>
  287. <script>
  288. Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
  289. var toc = jQuery('#toc');
  290. if (toc.length === 0 || !window.tocbot) { return; }
  291. var boardCtn = jQuery('#board-ctn');
  292. var boardTop = boardCtn.offset().top;
  293. window.tocbot.init(Object.assign({
  294. tocSelector : '#toc-body',
  295. contentSelector : '.markdown-body',
  296. linkClass : 'tocbot-link',
  297. activeLinkClass : 'tocbot-active-link',
  298. listClass : 'tocbot-list',
  299. isCollapsedClass: 'tocbot-is-collapsed',
  300. collapsibleClass: 'tocbot-is-collapsible',
  301. scrollSmooth : true,
  302. includeTitleTags: true,
  303. headingsOffset : -boardTop,
  304. }, CONFIG.toc));
  305. if (toc.find('.toc-list-item').length > 0) {
  306. toc.css('visibility', 'visible');
  307. }
  308. Fluid.events.registerRefreshCallback(function() {
  309. if ('tocbot' in window) {
  310. tocbot.refresh();
  311. var toc = jQuery('#toc');
  312. if (toc.length === 0 || !tocbot) {
  313. return;
  314. }
  315. if (toc.find('.toc-list-item').length > 0) {
  316. toc.css('visibility', 'visible');
  317. }
  318. }
  319. });
  320. });
  321. </script>
  322. <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
  323. <script>Fluid.plugins.codeWidget();</script>
  324. <script>
  325. Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
  326. window.anchors.options = {
  327. placement: CONFIG.anchorjs.placement,
  328. visible : CONFIG.anchorjs.visible
  329. };
  330. if (CONFIG.anchorjs.icon) {
  331. window.anchors.options.icon = CONFIG.anchorjs.icon;
  332. }
  333. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  334. var res = [];
  335. for (var item of el) {
  336. res.push('.markdown-body > ' + item.trim());
  337. }
  338. if (CONFIG.anchorjs.placement === 'left') {
  339. window.anchors.options.class = 'anchorjs-link-left';
  340. }
  341. window.anchors.add(res.join(', '));
  342. Fluid.events.registerRefreshCallback(function() {
  343. if ('anchors' in window) {
  344. anchors.removeAll();
  345. var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
  346. var res = [];
  347. for (var item of el) {
  348. res.push('.markdown-body > ' + item.trim());
  349. }
  350. if (CONFIG.anchorjs.placement === 'left') {
  351. anchors.options.class = 'anchorjs-link-left';
  352. }
  353. anchors.add(res.join(', '));
  354. }
  355. });
  356. });
  357. </script>
  358. <script>
  359. Fluid.utils.createScript('https://lib.baomitu.com/fancybox/3.5.7/jquery.fancybox.min.js', function() {
  360. Fluid.plugins.fancyBox();
  361. });
  362. </script>
  363. <script>Fluid.plugins.imageCaption();</script>
  364. <script src="/js/local-search.js" ></script>
  365. <!-- 主题的启动项,将它保持在最底部 -->
  366. <!-- the boot of the theme, keep it at the bottom -->
  367. <script src="/js/boot.js" ></script>
  368. <noscript>
  369. <div class="noscript-warning">Blog works best with JavaScript enabled</div>
  370. </noscript>
  371. <!-- hexo injector body_end start -->
  372. <script defer src="/theme-inject/timeliness.js"></script>
  373. <!-- hexo injector body_end end --></body>
  374. </html>