| 123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127128129130131132133134135136137138139140141142143144145146147148149150151152153154155156157158159160161162163164165166167168169170171172173174175176177178179180181182183184185186187188189190191192193194195196197198199200201202203204205206207208209210211212213214215216217218219220221222223224225226227228229230231232233234235236237238239240241242243244245246247248249250251252253254255256257258259260261262263264265266267268269270271272273274275276277278279280281282283284285286287288289290291292293294295296297298299300301302303304305306307308309310311312313314315316317318319320321322323324325326327328329330331332333334335336337338339340341342343344345346347348349350351352353354355356357358359360361362363364365366367368369370371372373374375376377378379380381382383384385386387388389390391392393394395396397398399400401402403404405406407408409410411412413414415416417418419420421422423424425426427428429430431432433434435436437438439440441442443444445446447448449450451452453454455456457458459460461462463464465466467468469470471472473474475476477478479480481482483484485486487488489490491492493494495496497498499500501502503504505506507508509510511512513514515516517518519520521522523524525526527528529530531532533534535536537538539540541542543544545546547548549550551552553554555556557558559560561562563564565566567568569570571572573574575576577578579580581582583584585586587588589590591592593594595596597598599600601602603604605606607608609610611612613614615616617618619620621622623624625626627628629630631632633634635636637638639640641642643644645646647648649650651652653654655656657658659660661662663664665666667668669670671672673674675676677678679680681682683684685686687688689690691692693694695696697698699700701702703704705706707708709710711712713714715716717718719720721722723724725726727728729730731732 |
- <!DOCTYPE html>
- <html lang="en" data-default-color-scheme=auto>
- <head><!-- hexo injector head_begin start -->
- <script defer src="https://api.limour.top/vue/0d2f95c1-755d-436b-adf8-eee12a80ed32/script.js"></script>
- <!-- hexo injector head_begin end -->
- <meta charset="UTF-8">
- <link rel="apple-touch-icon" sizes="76x76" href="https://img.limour.top/2023/08/29/64ee07361815a.webp">
- <link rel="icon" href="https://img.limour.top/2023/08/29/64ee07361815a.webp">
- <meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=5.0, shrink-to-fit=no">
- <meta http-equiv="x-ua-compatible" content="ie=edge">
-
- <meta name="theme-color" content="#2f4154">
- <meta name="author" content="Limour">
- <meta name="keywords" content="">
-
- <meta name="description" content="通过比对，我们得到了counts矩阵，接下来可以进行DEGs分析。此时如果我们有多组之间的对比，则可以使用RRA算法来聚合我们的结果。 RRA的安装 1234567891011121314151617181920conda create -n tcga -c conda-forge r-base=4.1.2 -yconda activate tcgaconda install -c conda-f">
-
-
-
- <title>【迁移】从差异基因到RRA聚合 - Limour's Blog</title>
- <link rel="stylesheet" href="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/css/bootstrap.min.css" />
- <link rel="stylesheet" href="https://jscdn.limour.top/npm/github-markdown-css@4.0.0/github-markdown.min.css" />
- <link rel="stylesheet" href="https://jscdn.limour.top/npm/hint.css@2.7.0/hint.min.css" />
- <!-- 主题依赖的图标库，不要自行修改 -->
- <!-- Do not modify the link that theme dependent icons -->
- <link rel="stylesheet" href="//at.alicdn.com/t/c/font_1749284_5i9bdhy70f8.css">
- <link rel="stylesheet" href="//at.alicdn.com/t/font_1736178_lbnruvf0jn.css">
- <link rel="stylesheet" href="/css/main.css" />
- <link id="highlight-css" rel="stylesheet" href="/css/highlight.css" />
-
- <link id="highlight-css-dark" rel="stylesheet" href="/css/highlight-dark.css" />
-
-
- <link rel="stylesheet" href="/theme-inject/custom.css">
- <link rel="stylesheet" href="/theme-inject/iconfont.css">
- <script id="fluid-configs">
- var Fluid = window.Fluid || {};
- Fluid.ctx = Object.assign({}, Fluid.ctx)
- var CONFIG = {"hostname":"hexo.limour.top","root":"/","version":"1.9.8","typing":{"enable":false,"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":false,"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},"leancloud":{"app_id":null,"app_key":null,"server_url":null,"path":"window.location.pathname","ignore_local":false},"umami":{"src":null,"website_id":null,"domains":null,"start_time":"2024-01-01T00:00:00.000Z","token":null,"api_server":null},"woyaola":null,"cnzz":null},"search_path":"/local-search.xml","include_content_in_search":true};
- if (CONFIG.web_analytics.follow_dnt) {
- var dntVal = navigator.doNotTrack || window.doNotTrack || navigator.msDoNotTrack;
- Fluid.ctx.dnt = dntVal && (dntVal.startsWith('1') || dntVal.startsWith('yes') || dntVal.startsWith('on'));
- }
- </script>
- <script src="/js/utils.js" ></script>
- <script src="/js/color-schema.js" ></script>
-
-
- <link rel="canonical" href="https://hexo.limour.top/cong-cha-yi-ji-yin-dao-RRA-ju-he"/>
- <meta name="generator" content="Hexo 7.1.1"><link rel="alternate" href="/atom.xml" title="Limour's Blog" type="application/atom+xml">
- <link rel="alternate" href="/rss2.xml" title="Limour's Blog" type="application/rss+xml">
- </head>
- <body>
-
- <header>
-
- <div class="header-inner" style="height: 70vh;">
- <nav id="navbar" class="navbar fixed-top navbar-expand-lg navbar-dark scrolling-navbar">
- <div class="container">
- <a class="navbar-brand" href="/">
- <strong>Limour's Blog</strong>
- </a>
- <button id="navbar-toggler-btn" class="navbar-toggler" type="button" data-toggle="collapse"
- data-target="#navbarSupportedContent"
- aria-controls="navbarSupportedContent" aria-expanded="false" aria-label="Toggle navigation">
- <div class="animated-icon"><span></span><span></span><span></span></div>
- </button>
- <!-- Collapsible content -->
- <div class="collapse navbar-collapse" id="navbarSupportedContent">
- <ul class="navbar-nav ml-auto text-center">
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="https://hexo.limour.top/" target="_self">
- <i class="iconfont icon-home-fill"></i>
- <span>Home</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="/archives/" target="_self">
- <i class="iconfont icon-archive-fill"></i>
- <span>Archive1</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="https://occdn.limour.top/archives/" target="_self">
- <i class="iconfont icon-archive-fill"></i>
- <span>Archive2</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="https://b.limour.top/archives/" target="_self">
- <i class="iconfont icon-archive-fill"></i>
- <span>Archive3</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="https://od.limour.top/" target="_self">
- <i class="iconfont icon-onedrive"></i>
- <span>Alist</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="https://orcid.org/0000-0001-8897-1685" target="_self">
- <i class="iconfont icon-orcid"></i>
- <span>Orcid</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="/links/" target="_self">
- <i class="iconfont icon-link-fill"></i>
- <span>Links</span>
- </a>
- </li>
-
-
-
-
-
-
- <li class="nav-item">
- <a class="nav-link" href="/atom.xml" target="_self">
- <i class="iconfont icon-rss"></i>
- <span>RSS</span>
- </a>
- </li>
-
-
-
- <li class="nav-item" id="search-btn">
- <a class="nav-link" target="_self" href="javascript:;" data-toggle="modal" data-target="#modalSearch" aria-label="Search">
- <i class="iconfont icon-search"></i>
- </a>
- </li>
-
-
-
- <li class="nav-item" id="color-toggle-btn">
- <a class="nav-link" target="_self" href="javascript:;" aria-label="Color Toggle">
- <i class="iconfont icon-dark" id="color-toggle-icon"></i>
- </a>
- </li>
-
- </ul>
- </div>
- </div>
- </nav>
-
- <div id="banner" class="banner" parallax=true
- style="background: url('https://img.limour.top/2023/08/29/64ee08e108638.webp') no-repeat center center; background-size: cover;">
- <div class="full-bg-img">
- <div class="mask flex-center" style="background-color: rgba(0, 0, 0, 0.3)">
- <div class="banner-text text-center fade-in-up">
- <div class="h2">
-
- <span id="subtitle">【迁移】从差异基因到RRA聚合</span>
-
- </div>
-
-
- <div class="mt-3">
-
- <span class="post-meta mr-2">
- <i class="iconfont icon-author" aria-hidden="true"></i>
- Limour
- </span>
-
-
- <span class="post-meta">
- <i class="iconfont icon-date-fill" aria-hidden="true"></i>
- <time datetime="2022-07-22 18:46" pubdate>
- July 22, 2022 pm
- </time>
- </span>
-
- </div>
- <div class="mt-1">
-
- <span class="post-meta mr-2">
- <i class="iconfont icon-chart"></i>
-
- 1.7k words
-
- </span>
-
-
- <span class="post-meta mr-2">
- <i class="iconfont icon-clock-fill"></i>
-
-
-
- 15 mins
-
- </span>
-
-
-
- </div>
-
- </div>
-
- </div>
- </div>
- </div>
- </div>
- </header>
- <main>
-
-
- <div class="container-fluid nopadding-x">
- <div class="row nomargin-x">
- <div class="side-col d-none d-lg-block col-lg-2">
-
- </div>
- <div class="col-lg-8 nopadding-x-md">
- <div class="container nopadding-x-md" id="board-ctn">
- <div id="board">
- <article class="post-content mx-auto">
- <h1 id="seo-header">【迁移】从差异基因到RRA聚合</h1>
-
- <p id="updated-time" class="note note-info" style="">
-
-
- Last updated on March 19, 2024 pm
-
-
- </p>
-
-
- <div class="markdown-body">
-
- <p>通过<a href="/STAR--yi-jian-jiao-ben">比对</a>，我们得到了counts矩阵，接下来可以进行DEGs分析。此时如果我们有多组之间的对比，则可以使用RRA算法来聚合我们的结果。</p>
- <h2 id="RRA的安装">RRA的安装</h2>
- <figure class="highlight bash"><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 bash">conda create -n tcga -c conda-forge r-base=4.1.2 -y<br>conda activate tcga<br>conda install -c conda-forge r-rvest=1.0.2 -y<br>conda install -c conda-forge r-xml=3.99_0.8 -y<br>conda install -c conda-forge r-rcpparmadillo=0.10.8.1.0 -y<br>conda install -c conda-forge r-bh=1.78.0_0 -y<br>conda install -c conda-forge r-biocmanager=1.30.16 -y<br>conda install -c bioconda bioconductor-summarizedexperiment=1.24.0 -y<br>conda install -c bioconda bioconductor-tcgabiolinks=2.22.1 -y<br>conda install -c bioconda bioconductor-deseq2=1.34.0 -y<br>conda install -c bioconda bioconductor-rhdf5=2.38.0 -y<br>conda install -c bioconda bioconductor-limma=3.50.1 -y<br>conda install -c bioconda bioconductor-apeglm=1.16.0 -y<br>conda install -c bioconda r-sleuth=0.30.0 -y<br>conda install -c bioconda r-wasabi=1.0.1 -y<br>conda install -c conda-forge r-irkernel=1.3 -y<br>conda install -c conda-forge r-ashr=2.2_54 -y<br>conda install -c conda-forge r-robustrankaggreg=1.1 -y<br>conda install -c conda-forge r-devtools=2.4.3 -y<br>IRkernel::installspec(name=<span class="hljs-string">'tcga'</span>, displayname=<span class="hljs-string">'r-tcga'</span>)<br></code></pre></td></tr></table></figure>
- <ul>
- <li>deseq2 数据要求：低生物学重复 & raw counts；假定负二项分布；适合高通量测序数据</li>
- <li>sleuth 数据要求：<strong>Kallisto</strong>输出的结果</li>
- <li>limma 数据要求：logCPM；假定正态分布；适合芯片数据</li>
- <li><a href="https://hexo.limour.top/go/#aHR0cHM6Ly9iaW9jb25kdWN0b3Iub3JnL3BhY2thZ2VzL3JlbGVhc2UvYmlvYy92aWduZXR0ZXMvbGltbWEvaW5zdC9kb2MvdXNlcnNndWlkZS5wZGY=" rel="noopener external nofollow noreferrer">fpkm数据差异基因分析</a> ：理论上是不能进行分析的，无计可施时可以参考</li>
- <li>高生物学重复请直接使用 <strong>wilcox.test</strong> 以避免大量假阳性</li>
- <li>多数据集结果整合：RobustRankAggreg</li>
- </ul>
- <p>fpkm转tpm示例（基于 SummarizedExperiment 数据框架）</p>
- <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">fpkmToTpm <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>fpkm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> <span class="hljs-built_in">exp</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span>fpkm<span class="hljs-punctuation">)</span> <span class="hljs-operator">-</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>fpkm<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span> <span class="hljs-built_in">log</span><span class="hljs-punctuation">(</span><span class="hljs-number">1e6</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br>f_fpkmToTpm <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>l_e<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> apply<span class="hljs-punctuation">(</span>l_e<span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span>fpkmToTpm<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br>assay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">"TPM"</span><span class="hljs-punctuation">)</span> <span class="hljs-operator"><-</span> f_fpkmToTpm<span class="hljs-punctuation">(</span>assay<span class="hljs-punctuation">(</span>sce<span class="hljs-punctuation">,</span> <span class="hljs-string">"HTSeq - FPKM"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第一步，多组差异基因分析">第一步，多组差异基因分析</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></pre></td><td class="code"><pre><code class="hljs R">library<span class="hljs-punctuation">(</span>DESeq2<span class="hljs-punctuation">)</span><br>count_all <span class="hljs-operator"><-</span> read.csv<span class="hljs-punctuation">(</span><span class="hljs-string">"~/upload/zl_liu/star_data/yyz_01/yyz_01.csv"</span><span class="hljs-punctuation">,</span>header<span class="hljs-operator">=</span><span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br>count_all<br>cts_b <span class="hljs-operator"><-</span> count_all<span class="hljs-punctuation">[</span> <span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-operator">-</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br>rownames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span> <span class="hljs-operator"><-</span> count_all<span class="hljs-operator">$</span>ID<br>keep <span class="hljs-operator"><-</span> rowSums<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span> <span class="hljs-operator">></span> ncol<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><br>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br>f_DESeq2 <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>cts_bb<span class="hljs-punctuation">,</span> rowInfo<span class="hljs-punctuation">,</span> ControlN<span class="hljs-punctuation">,</span> TreatN<span class="hljs-punctuation">,</span> rm.NA<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> cts_b <span class="hljs-operator"><-</span> cts_bb<span class="hljs-punctuation">[</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">,</span> TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><br> conditions <span class="hljs-operator"><-</span> factor<span class="hljs-punctuation">(</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">"Control"</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span><span class="hljs-string">"Treat"</span><span class="hljs-punctuation">,</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>TreatN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span> <br> colData_b <span class="hljs-operator"><-</span> data.frame<span class="hljs-punctuation">(</span>row.names <span class="hljs-operator">=</span> colnames<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> conditions<span class="hljs-punctuation">)</span><br> print<span class="hljs-punctuation">(</span>colData_b<span class="hljs-punctuation">)</span><br> dds <span class="hljs-operator"><-</span> DESeqDataSetFromMatrix<span class="hljs-punctuation">(</span>countData <span class="hljs-operator">=</span> cts_b<span class="hljs-punctuation">,</span><br> colData <span class="hljs-operator">=</span> colData_b<span class="hljs-punctuation">,</span><br> design <span class="hljs-operator">=</span> <span class="hljs-operator">~</span> conditions<span class="hljs-punctuation">)</span><br> dds <span class="hljs-operator"><-</span> DESeq<span class="hljs-punctuation">(</span>dds<span class="hljs-punctuation">)</span><br> res <span class="hljs-operator"><-</span> results<span class="hljs-punctuation">(</span>dds<span class="hljs-punctuation">)</span><br> rres <span class="hljs-operator"><-</span> cbind<span class="hljs-punctuation">(</span>rowInfo<span class="hljs-punctuation">,</span> data.frame<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>rm.NA<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span>rres <span class="hljs-operator"><-</span> rres<span class="hljs-punctuation">[</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.na</span><span class="hljs-punctuation">(</span>rres<span class="hljs-operator">$</span>padj<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">}</span><br> rres <span class="hljs-operator"><-</span> rres<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>rres<span class="hljs-operator">$</span>log2FoldChange<span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br> saveRDS<span class="hljs-punctuation">(</span>rres<span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span><span class="hljs-string">'DEGs'</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>TreatN<span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">'_'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'vs.'</span><span class="hljs-punctuation">,</span> paste<span class="hljs-punctuation">(</span>ControlN<span class="hljs-punctuation">,</span> collapse <span class="hljs-operator">=</span> <span class="hljs-string">'_'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'DESeq2.rds'</span><span class="hljs-punctuation">,</span>sep <span class="hljs-operator">=</span> <span class="hljs-string">'_'</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> rres<br><span class="hljs-punctuation">}</span><br>Ct1 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.control.DMSO'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.control.DMSO'</span><span class="hljs-punctuation">)</span><br>Tt1 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.OE.DMSO'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.OE.DMSO'</span><span class="hljs-punctuation">)</span><br>Ct2 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.OE.DMSO'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.OE.DMSO'</span><span class="hljs-punctuation">)</span><br>Tt2 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.OE.Enz'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.OE.Enz'</span><span class="hljs-punctuation">)</span><br>Ct3 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.control.Enz'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.control.Enz'</span><span class="hljs-punctuation">)</span><br>Tt3 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.OE.Enz'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.OE.Enz'</span><span class="hljs-punctuation">)</span><br>Ct4 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.CAF.DMSO'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.CAF.DMSO'</span><span class="hljs-punctuation">)</span><br>Tt4 <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'X1.CAF.Enz'</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'X2.CAF.Enz'</span><span class="hljs-punctuation">)</span><br>r1 <span class="hljs-operator"><-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct1<span class="hljs-punctuation">,</span> Tt1<span class="hljs-punctuation">)</span><br>r2 <span class="hljs-operator"><-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct2<span class="hljs-punctuation">,</span> Tt2<span class="hljs-punctuation">)</span><br>r3 <span class="hljs-operator"><-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct3<span class="hljs-punctuation">,</span> Tt3<span class="hljs-punctuation">)</span><br>r4 <span class="hljs-operator"><-</span> f_DESeq2<span class="hljs-punctuation">(</span>cts_b<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> count_all<span class="hljs-punctuation">[</span>keep<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> Ct4<span class="hljs-punctuation">,</span> Tt4<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="第二步，RRA聚合差异结果">第二步，RRA聚合差异结果</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></pre></td><td class="code"><pre><code class="hljs R">require<span class="hljs-punctuation">(</span>RobustRankAggreg<span class="hljs-punctuation">)</span><br>f_dflist_RRA <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">,</span> N<span class="hljs-punctuation">,</span> orderN<span class="hljs-punctuation">,</span> decreasing<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</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>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> tmp <span class="hljs-operator"><-</span> dflist<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> tmp<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">}</span><span class="hljs-keyword">else</span> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">>=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> tmp<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[[</span>orderN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>decreasing <span class="hljs-operator">=</span> decreasing<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator"><</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span> <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><br> aggregateRanks<span class="hljs-punctuation">(</span>glist <span class="hljs-operator">=</span> res<span class="hljs-punctuation">,</span> N <span class="hljs-operator">=</span> N<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br>rownames<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">)</span> <span class="hljs-operator"><-</span> count_all<span class="hljs-operator">$</span>ID<br> <br>r <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>r1<span class="hljs-operator">=</span>r1<span class="hljs-punctuation">,</span>r2<span class="hljs-operator">=</span>r2<span class="hljs-punctuation">,</span>r3<span class="hljs-operator">=</span>r3<span class="hljs-punctuation">,</span>r4<span class="hljs-operator">=</span>r4<span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> lapply<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> padj<span class="hljs-operator"><</span><span class="hljs-number">0.05</span> <span class="hljs-operator">&</span> log2FoldChange <span class="hljs-operator">></span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">'ID'</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>keep<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'log2FoldChange'</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> cbind<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">[</span>r<span class="hljs-operator">$</span>Name<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> r<span class="hljs-punctuation">)</span><br>r<br>write.csv<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">'RRA_up.csv'</span><span class="hljs-punctuation">)</span><br> <br>r <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>r1<span class="hljs-operator">=</span>r1<span class="hljs-punctuation">,</span>r2<span class="hljs-operator">=</span>r2<span class="hljs-punctuation">,</span>r3<span class="hljs-operator">=</span>r3<span class="hljs-punctuation">,</span>r4<span class="hljs-operator">=</span>r4<span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> lapply<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> padj<span class="hljs-operator"><</span><span class="hljs-number">0.05</span> <span class="hljs-operator">&</span> log2FoldChange <span class="hljs-operator"><</span> <span class="hljs-operator">-</span><span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">'ID'</span><span class="hljs-punctuation">,</span> <span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>keep<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'log2FoldChange'</span><span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">F</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> cbind<span class="hljs-punctuation">(</span>count_all<span class="hljs-punctuation">[</span>r<span class="hljs-operator">$</span>Name<span class="hljs-punctuation">,</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">2</span><span class="hljs-punctuation">,</span><span class="hljs-number">3</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> r<span class="hljs-punctuation">)</span><br>r<br>write.csv<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> <span class="hljs-string">'RRA_down.csv'</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="附加：绘图">附加：绘图</h2>
- <h3 id="安装包">安装包</h3>
- <figure class="highlight bash"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs bash">conda create -n rsf -c conda-forge r-sf=1.0_4<br>conda activate rsf<br>library(sf)<br><span class="hljs-comment"># install.packages("sf", version = "1.0-4")</span><br>install.packages(<span class="hljs-string">"ggVennDiagram"</span>)<br>conda install -c conda-forge r-ggsci -y<br>conda install -c conda-forge r-irkernel -y<br>Rscript -e <span class="hljs-string">"IRkernel::installspec(name='ggVennDiagram', displayname='r-ggVennDiagram')"</span><br>conda install -c conda-forge r-venndiagram -y<br></code></pre></td></tr></table></figure>
- <h3 id="数据准备">数据准备</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></pre></td><td class="code"><pre><code class="hljs R">x <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>r <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br>r<span class="hljs-operator">$</span>cell <span class="hljs-operator"><-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">'../A_ref_A_fiig.1_A/DEG.rds'</span><span class="hljs-punctuation">)</span><br>r<span class="hljs-operator">$</span>tissue <span class="hljs-operator"><-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">'../B_ref_A_fiig.1_A/DEG.rds'</span><span class="hljs-punctuation">)</span><br><span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>r<span class="hljs-operator">$</span>tissue<span class="hljs-punctuation">)</span><span class="hljs-punctuation">[</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> <span class="hljs-string">'symbol'</span><br>r_up <span class="hljs-operator"><-</span> lapply<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> log2FoldChange <span class="hljs-operator">></span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><br>x<span class="hljs-operator">$</span>cell_up <span class="hljs-operator"><-</span> r_up<span class="hljs-operator">$</span>cell<span class="hljs-operator">$</span>symbol<br>x<span class="hljs-operator">$</span>RRA_up <span class="hljs-operator"><-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">'r_up.rds'</span><span class="hljs-punctuation">)</span><br>x<span class="hljs-operator">$</span>RRA_up <span class="hljs-operator"><-</span> x<span class="hljs-operator">$</span>RRA_up<span class="hljs-operator">$</span>Name<br>x<span class="hljs-operator">$</span>tissue_up <span class="hljs-operator"><-</span> r_up<span class="hljs-operator">$</span>tissue<span class="hljs-operator">$</span>symbol<br>r_dn <span class="hljs-operator"><-</span> lapply<span class="hljs-punctuation">(</span>r<span class="hljs-punctuation">,</span> FUN <span class="hljs-operator">=</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span>subset<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">,</span> log2FoldChange <span class="hljs-operator"><</span> <span class="hljs-number">0</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><span class="hljs-punctuation">)</span><br>x<span class="hljs-operator">$</span>cell_down <span class="hljs-operator"><-</span> r_dn<span class="hljs-operator">$</span>cell<span class="hljs-operator">$</span>symbol<br>x<span class="hljs-operator">$</span>RRA_down <span class="hljs-operator"><-</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">'r_dn.rds'</span><span class="hljs-punctuation">)</span><br>x<span class="hljs-operator">$</span>RRA_down <span class="hljs-operator"><-</span> x<span class="hljs-operator">$</span>RRA_down<span class="hljs-operator">$</span>Name<br>x<span class="hljs-operator">$</span>tissue_down <span class="hljs-operator"><-</span> r_dn<span class="hljs-operator">$</span>tissue<span class="hljs-operator">$</span>symbol<br>summary<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h3 id="绘图1">绘图1</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></pre></td><td class="code"><pre><code class="hljs R"><span class="hljs-comment">#载入所需的R包；</span><br>library<span class="hljs-punctuation">(</span>ggplot2<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggsci<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>sf<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>ggVennDiagram<span class="hljs-punctuation">)</span><br>color4 <span class="hljs-operator"><-</span> alpha<span class="hljs-punctuation">(</span><span class="hljs-string">"#99CC00"</span><span class="hljs-punctuation">,</span><span class="hljs-number">0.5</span><span class="hljs-punctuation">)</span><br>ggVennDiagram<span class="hljs-punctuation">(</span>x<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">6</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> label_alpha<span class="hljs-operator">=</span><span class="hljs-number">0</span><span class="hljs-punctuation">)</span> <span class="hljs-operator">+</span><br> scale_fill_gradient<span class="hljs-punctuation">(</span>low<span class="hljs-operator">=</span><span class="hljs-string">'white'</span><span class="hljs-punctuation">,</span>high <span class="hljs-operator">=</span>color4<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h3 id="绘图2">绘图2</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></pre></td><td class="code"><pre><code class="hljs R">venn.plot <span class="hljs-operator"><-</span> venn.diagram<span class="hljs-punctuation">(</span><br> x <span class="hljs-operator">=</span> x<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-operator">:</span><span class="hljs-number">3</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br> filename <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span><br> cex <span class="hljs-operator">=</span> <span class="hljs-number">2.5</span><span class="hljs-punctuation">,</span><br> cat.cex <span class="hljs-operator">=</span> <span class="hljs-number">2.5</span><span class="hljs-punctuation">,</span><br> cat.dist <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0.07</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0.07</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0.02</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> cat.pos <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">20</span><span class="hljs-punctuation">,</span> <span class="hljs-number">20</span><span class="hljs-punctuation">,</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> alpha <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span><br> fill <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"#99CC00"</span><span class="hljs-punctuation">,</span> <span class="hljs-string">"#c77cff"</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'#f8766d'</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">)</span>;<br>grid.draw<span class="hljs-punctuation">(</span>venn.plot<span class="hljs-punctuation">)</span><br>venn.plot <span class="hljs-operator"><-</span> venn.diagram<span class="hljs-punctuation">(</span><br> x <span class="hljs-operator">=</span> x<span class="hljs-punctuation">[</span><span class="hljs-number">4</span><span class="hljs-operator">:</span><span class="hljs-number">6</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span><br> filename <span class="hljs-operator">=</span> <span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span><br> cex <span class="hljs-operator">=</span> <span class="hljs-number">2.5</span><span class="hljs-punctuation">,</span><br> cat.cex <span class="hljs-operator">=</span> <span class="hljs-number">2.5</span><span class="hljs-punctuation">,</span><br> cat.dist <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-number">0.07</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0.07</span><span class="hljs-punctuation">,</span> <span class="hljs-number">0.02</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> cat.pos <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-operator">-</span><span class="hljs-number">20</span><span class="hljs-punctuation">,</span> <span class="hljs-number">20</span><span class="hljs-punctuation">,</span> <span class="hljs-number">20</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><br> alpha <span class="hljs-operator">=</span> <span class="hljs-number">0.5</span><span class="hljs-punctuation">,</span><br> fill <span class="hljs-operator">=</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"#99CC00"</span><span class="hljs-punctuation">,</span> <span class="hljs-string">"#c77cff"</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'#f8766d'</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">)</span>;<br>grid.draw<span class="hljs-punctuation">(</span>venn.plot<span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h2 id="附加：单细胞数据">附加：单细胞数据</h2>
- <h3 id="第一步-读取数据">第一步 读取数据</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><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><span class="line">38</span><br><span class="line">39</span><br><span class="line">40</span><br><span class="line">41</span><br><span class="line">42</span><br><span class="line">43</span><br><span class="line">44</span><br><span class="line">45</span><br></pre></td><td class="code"><pre><code class="hljs r">library<span class="hljs-punctuation">(</span>Seurat<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>plyr<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>dplyr<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>patchwork<span class="hljs-punctuation">)</span><br>library<span class="hljs-punctuation">(</span>purrr<span class="hljs-punctuation">)</span><br>f_metadata_removeNA <span class="hljs-operator"><-</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">{</span><br> sObject<span class="hljs-operator">@</span>meta.data <span class="hljs-operator"><-</span> sObject<span class="hljs-operator">@</span>meta.data<span class="hljs-punctuation">[</span>colnames<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span><span class="hljs-punctuation">]</span><br> sObject <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> sObject<span class="hljs-punctuation">,</span> <span class="hljs-operator">!</span><span class="hljs-operator">!</span>sym<span class="hljs-punctuation">(</span>lc_groupN<span class="hljs-punctuation">)</span><span class="hljs-operator">%in%</span>f_br_cluster_f<span class="hljs-punctuation">(</span>sObject<span class="hljs-punctuation">,</span> lc_groupN<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> sObject<br><span class="hljs-punctuation">}</span><br>f_br_cluster_f <span class="hljs-operator"><-</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">{</span><br> lc_filter <span class="hljs-operator"><-</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"><-</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">}</span><br><br>scRNA_split <span class="hljs-operator">=</span> readRDS<span class="hljs-punctuation">(</span><span class="hljs-string">"~/zlliu/R_output/21.09.21.SingleR/scRNA.rds"</span><span class="hljs-punctuation">)</span><br>scRNA_split <span class="hljs-operator"><-</span> f_metadata_removeNA<span class="hljs-punctuation">(</span>scRNA_split<span class="hljs-punctuation">,</span> <span class="hljs-string">'Region'</span><span class="hljs-punctuation">)</span><br><br>n_ExN <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'L4 IT'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L5 IT'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L5 ET'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'IT'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L6b'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L5/6 IT Car3'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L6 IT'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L2/3 IT'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L5/6 NP'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L6 IT Car3'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'L6 CT'</span><span class="hljs-punctuation">)</span><br>n_InN <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'Lamp5'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Pvalb'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Sst'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Vip'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Sncg'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'PAX6'</span><span class="hljs-punctuation">)</span><br>n_NoN <span class="hljs-operator"><-</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">'Astro'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Endo'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Micro-PVM'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'OPC'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Oligo'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'Pericyte'</span><span class="hljs-punctuation">,</span><span class="hljs-string">'VLMC'</span><span class="hljs-punctuation">)</span><br>n_groups <span class="hljs-operator"><-</span> <span class="hljs-built_in">list</span><span class="hljs-punctuation">(</span>NoN<span class="hljs-operator">=</span>n_NoN<span class="hljs-punctuation">,</span> ExN<span class="hljs-operator">=</span>n_ExN<span class="hljs-punctuation">,</span> InN<span class="hljs-operator">=</span>n_InN<span class="hljs-punctuation">)</span><br><br>f_listUpdateRe <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_obj<span class="hljs-punctuation">,</span> lc_bool<span class="hljs-punctuation">,</span> lc_item<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> lc_obj<span class="hljs-punctuation">[</span>lc_bool<span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> <span class="hljs-built_in">rep</span><span class="hljs-punctuation">(</span>lc_item<span class="hljs-punctuation">,</span>times<span class="hljs-operator">=</span><span class="hljs-built_in">sum</span><span class="hljs-punctuation">(</span>lc_bool<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br> lc_obj<br><span class="hljs-punctuation">}</span><br>f_grouplabel <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">,</span> lc_groups<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</span> lc_meta.data<span class="hljs-punctuation">[[</span><span class="hljs-number">1</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>lc_g <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>lc_groups<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> lc_bool <span class="hljs-operator">=</span> <span class="hljs-punctuation">(</span>res <span class="hljs-operator">%in%</span> lc_groups<span class="hljs-punctuation">[[</span>lc_g<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>c_n <span class="hljs-keyword">in</span> colnames<span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> lc_bool <span class="hljs-operator">=</span> lc_bool <span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">[[</span>c_n<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">%in%</span> lc_groups<span class="hljs-punctuation">[[</span>lc_g<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> res <span class="hljs-operator"><-</span> f_listUpdateRe<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> lc_bool<span class="hljs-punctuation">,</span> lc_g<span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator"><-</span> rownames<span class="hljs-punctuation">(</span>lc_meta.data<span class="hljs-punctuation">)</span><br> res<br><span class="hljs-punctuation">}</span><br><br>scRNA_split<span class="hljs-punctuation">[[</span><span class="hljs-string">'n_groups'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> f_grouplabel<span class="hljs-punctuation">(</span>scRNA_split<span class="hljs-punctuation">[[</span><span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"hM1_hmca_class"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> n_groups<span class="hljs-punctuation">)</span><br>sc_Neuron <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>x <span class="hljs-operator">=</span> scRNA_split<span class="hljs-punctuation">,</span> n_groups <span class="hljs-operator">%in%</span> <span class="hljs-built_in">c</span><span class="hljs-punctuation">(</span><span class="hljs-string">"InN"</span><span class="hljs-punctuation">,</span> <span class="hljs-string">"ExN"</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><br><br>samples <span class="hljs-operator"><-</span> SplitObject<span class="hljs-punctuation">(</span>object <span class="hljs-operator">=</span> sc_Neuron<span class="hljs-punctuation">,</span> split.by <span class="hljs-operator">=</span> <span class="hljs-string">'orig.ident'</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
- <h3 id="第二步-计算差异基因">第二步 计算差异基因</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></pre></td><td class="code"><pre><code class="hljs r">DEGs <span class="hljs-operator"><-</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>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>samples<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> tmp <span class="hljs-operator"><-</span> samples<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> Idents<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator"><-</span> <span class="hljs-string">'Region'</span><br> DEGs<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator">=</span> FindAllMarkers<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> only.pos <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br></code></pre></td></tr></table></figure>
- <h3 id="第三步-整合数据">第三步 整合数据</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><span class="line">8</span><br><span class="line">9</span><br><span class="line">10</span><br><span class="line">11</span><br><span class="line">12</span><br><span class="line">13</span><br><span class="line">14</span><br><span class="line">15</span><br><span class="line">16</span><br><span class="line">17</span><br><span class="line">18</span><br><span class="line">19</span><br><span class="line">20</span><br><span class="line">21</span><br></pre></td><td class="code"><pre><code class="hljs r">f_dflist_subset <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">,</span> nameN<span class="hljs-operator">=</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</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>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> subset<span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span> ...<span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br> res<br><span class="hljs-punctuation">}</span><br>require<span class="hljs-punctuation">(</span>RobustRankAggreg<span class="hljs-punctuation">)</span><br>f_dflist_RRA <span class="hljs-operator"><-</span> <span class="hljs-keyword">function</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">,</span> N<span class="hljs-punctuation">,</span> orderN<span class="hljs-punctuation">,</span> decreasing<span class="hljs-operator">=</span><span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res <span class="hljs-operator"><-</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>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>dflist<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> tmp <span class="hljs-operator"><-</span> dflist<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><br> <span class="hljs-keyword">if</span> <span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">==</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> tmp<span class="hljs-punctuation">[</span><span class="hljs-number">1</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">}</span><span class="hljs-keyword">else</span> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span>nrow<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span> <span class="hljs-operator">>=</span><span class="hljs-number">2</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> res<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> tmp<span class="hljs-punctuation">[</span>order<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">[[</span>orderN<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">,</span>decreasing <span class="hljs-operator">=</span> decreasing<span class="hljs-punctuation">)</span><span class="hljs-punctuation">,</span> nameN<span class="hljs-punctuation">]</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-punctuation">}</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-built_in">length</span><span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">)</span> <span class="hljs-operator"><</span> <span class="hljs-number">1</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span> <span class="hljs-built_in">return</span><span class="hljs-punctuation">(</span><span class="hljs-literal">NULL</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">}</span><br> aggregateRanks<span class="hljs-punctuation">(</span>glist <span class="hljs-operator">=</span> res<span class="hljs-punctuation">,</span> N <span class="hljs-operator">=</span> N<span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br></code></pre></td></tr></table></figure>
- <figure class="highlight r"><table><tr><td class="gutter"><pre><span class="line">1</span><br><span class="line">2</span><br><span class="line">3</span><br><span class="line">4</span><br><span class="line">5</span><br><span class="line">6</span><br><span class="line">7</span><br><span class="line">8</span><br><span class="line">9</span><br></pre></td><td class="code"><pre><code class="hljs r">res <span class="hljs-operator"><-</span> data.frame<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span><span class="hljs-punctuation">(</span>name <span class="hljs-keyword">in</span> unique<span class="hljs-punctuation">(</span>sc_Neuron<span class="hljs-operator">@</span>meta.data<span class="hljs-operator">$</span>Region<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> tmp <span class="hljs-operator"><-</span> f_dflist_subset<span class="hljs-punctuation">(</span>DEGs<span class="hljs-punctuation">,</span> name<span class="hljs-punctuation">,</span> cluster<span class="hljs-operator">==</span>nameN<span class="hljs-punctuation">)</span><br> tmp <span class="hljs-operator"><-</span> f_dflist_RRA<span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">,</span> <span class="hljs-string">'gene'</span><span class="hljs-punctuation">,</span> N<span class="hljs-operator">=</span><span class="hljs-number">24223</span><span class="hljs-punctuation">,</span> <span class="hljs-string">'avg_log2FC'</span><span class="hljs-punctuation">,</span> decreasing <span class="hljs-operator">=</span> <span class="hljs-built_in">T</span><span class="hljs-punctuation">)</span><br> <span class="hljs-keyword">if</span><span class="hljs-punctuation">(</span><span class="hljs-operator">!</span><span class="hljs-built_in">is.null</span><span class="hljs-punctuation">(</span>tmp<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> tmp<span class="hljs-punctuation">[[</span><span class="hljs-string">'cluster'</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span> <span class="hljs-operator"><-</span> name<br> res <span class="hljs-operator"><-</span> rbind<span class="hljs-punctuation">(</span>res<span class="hljs-punctuation">,</span> tmp<span class="hljs-punctuation">)</span><br> <span class="hljs-punctuation">}</span><br><span class="hljs-punctuation">}</span><br></code></pre></td></tr></table></figure>
- <h3 id="第四步-保存结果">第四步 保存结果</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></pre></td><td class="code"><pre><code class="hljs r">require<span class="hljs-punctuation">(</span>openxlsx<span class="hljs-punctuation">)</span><br>wb <span class="hljs-operator"><-</span> createWorkbook<span class="hljs-punctuation">(</span><span class="hljs-punctuation">)</span><br><span class="hljs-keyword">for</span> <span class="hljs-punctuation">(</span>name <span class="hljs-keyword">in</span> <span class="hljs-built_in">names</span><span class="hljs-punctuation">(</span>samples<span class="hljs-punctuation">)</span><span class="hljs-punctuation">)</span><span class="hljs-punctuation">{</span><br> addWorksheet<span class="hljs-punctuation">(</span>wb <span class="hljs-operator">=</span> wb<span class="hljs-punctuation">,</span> sheetName <span class="hljs-operator">=</span> name<span class="hljs-punctuation">)</span><br> writeData<span class="hljs-punctuation">(</span>wb <span class="hljs-operator">=</span> wb<span class="hljs-punctuation">,</span> sheet <span class="hljs-operator">=</span> name<span class="hljs-punctuation">,</span> x <span class="hljs-operator">=</span> DEGs<span class="hljs-punctuation">[[</span>name<span class="hljs-punctuation">]</span><span class="hljs-punctuation">]</span><span class="hljs-punctuation">)</span><br><span class="hljs-punctuation">}</span><br>addWorksheet<span class="hljs-punctuation">(</span>wb <span class="hljs-operator">=</span> wb<span class="hljs-punctuation">,</span> sheetName <span class="hljs-operator">=</span> <span class="hljs-string">'RRA'</span><span class="hljs-punctuation">)</span><br>writeData<span class="hljs-punctuation">(</span>wb <span class="hljs-operator">=</span> wb<span class="hljs-punctuation">,</span> sheet <span class="hljs-operator">=</span> <span class="hljs-string">'RRA'</span><span class="hljs-punctuation">,</span> x <span class="hljs-operator">=</span> res<span class="hljs-punctuation">)</span><br>saveWorkbook<span class="hljs-punctuation">(</span>wb<span class="hljs-punctuation">,</span> <span class="hljs-string">"DEG_Brain_Regin_Neuron.xlsx"</span><span class="hljs-punctuation">,</span> overwrite <span class="hljs-operator">=</span> <span class="hljs-literal">TRUE</span><span class="hljs-punctuation">)</span><br></code></pre></td></tr></table></figure>
-
- </div>
-
- <hr/>
- <div>
- <div class="post-metas my-3">
-
-
- <div class="post-meta">
- <i class="iconfont icon-tags"></i>
-
- <a href="/tags/degs/" class="print-no-link">#DEGs</a>
-
- <a href="/tags/rra/" class="print-no-link">#RRA</a>
-
- </div>
-
- </div>
-
-
- <div class="license-box my-3">
- <div class="license-title">
- <div>【迁移】从差异基因到RRA聚合</div>
- <div>https://hexo.limour.top/cong-cha-yi-ji-yin-dao-RRA-ju-he</div>
- </div>
- <div class="license-meta">
-
- <div class="license-meta-item">
- <div>Author</div>
- <div>Limour</div>
- </div>
-
-
- <div class="license-meta-item license-meta-date">
- <div>Posted on</div>
- <div>July 22, 2022</div>
- </div>
-
-
- <div class="license-meta-item license-meta-date">
- <div>Updated on</div>
- <div>March 19, 2024</div>
- </div>
-
-
- <div class="license-meta-item">
- <div>Licensed under</div>
- <div>
-
-
-
- <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
- <span class="hint--top hint--rounded" aria-label="BY - Attribution">
- <i class="iconfont icon-cc-by"></i>
- </span>
- </a>
-
- <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
- <span class="hint--top hint--rounded" aria-label="NC - Non-commercial">
- <i class="iconfont icon-cc-nc"></i>
- </span>
- </a>
-
- <a class="print-no-link" target="_blank" href="https://creativecommons.org/licenses/by-nc-sa/4.0/">
- <span class="hint--top hint--rounded" aria-label="SA - Share-alike">
- <i class="iconfont icon-cc-sa"></i>
- </span>
- </a>
-
-
- </div>
- </div>
-
- </div>
- <div class="license-icon iconfont"></div>
- </div>
-
- <div class="post-prevnext my-3">
- <article class="post-prev col-6">
-
-
- <a href="/Counts-ju-zhen-de-biao-zhun-hua-fang-fa--TMM-he-VST-RLOG" title="【迁移】Counts矩阵的标准化方法：TMM和VST、RLOG">
- <i class="iconfont icon-arrowleft"></i>
- <span class="hidden-mobile">【迁移】Counts矩阵的标准化方法：TMM和VST、RLOG</span>
- <span class="visible-mobile">Previous</span>
- </a>
-
- </article>
- <article class="post-next col-6">
-
-
- <a href="/Forest-plot-displays-the-results-of-regression-analysis" title="【迁移】森林图展示回归分析的结果">
- <span class="hidden-mobile">【迁移】森林图展示回归分析的结果</span>
- <span class="visible-mobile">Next</span>
- <i class="iconfont icon-arrowright"></i>
- </a>
-
- </article>
- </div>
-
- </div>
-
-
-
- <article id="comments" lazyload>
-
- <div id="waline"></div>
- <script type="text/javascript">
- Fluid.utils.loadComments('#waline', function() {
- Fluid.utils.createCssLink('https://cdn.staticfile.org/waline/2.15.5/waline.css')
- Fluid.utils.createScript('https://cdn.staticfile.org/waline/2.15.5/waline.js', function() {
- var options = Object.assign(
- {"serverURL":"https://comments.limour.top","path":"window.location.pathname","meta":["nick","mail","link"],"requiredMeta":["nick"],"lang":"zh-CN","emoji":["https://jscdn.limour.top/gh/walinejs/emojis/weibo"],"dark":"html[data-user-color-scheme=\"dark\"]","wordLimit":0,"pageSize":10},
- {
- el: '#waline',
- path: window.location.pathname
- }
- )
- Waline.init(options);
- Fluid.utils.waitElementVisible('#waline .vcontent', () => {
- var imgSelector = '#waline .vcontent img:not(.vemoji)';
- Fluid.plugins.imageCaption(imgSelector);
- Fluid.plugins.fancyBox(imgSelector);
- })
- });
- });
- </script>
- <noscript>Please enable JavaScript to view the comments</noscript>
- </article>
-
- </article>
- </div>
- </div>
- </div>
- <div class="side-col d-none d-lg-block col-lg-2">
-
- <aside class="sidebar" style="margin-left: -1rem">
- <div id="toc">
- <p class="toc-header">
- <i class="iconfont icon-list"></i>
- <span>Table of Contents</span>
- </p>
- <div class="toc-body" id="toc-body"></div>
- </div>
- </aside>
- </div>
- </div>
- </div>
-
-
-
-
-
-
- <a id="scroll-top-button" aria-label="TOP" href="#" role="button">
- <i class="iconfont icon-arrowup" aria-hidden="true"></i>
- </a>
-
-
- <div class="modal fade" id="modalSearch" tabindex="-1" role="dialog" aria-labelledby="ModalLabel"
- aria-hidden="true">
- <div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
- <div class="modal-content">
- <div class="modal-header text-center">
- <h4 class="modal-title w-100 font-weight-bold">Search</h4>
- <button type="button" id="local-search-close" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
- <div class="modal-body mx-3">
- <div class="md-form mb-5">
- <input type="text" id="local-search-input" class="form-control validate">
- <label data-error="x" data-success="v" for="local-search-input">Keyword</label>
- </div>
- <div class="list-group" id="local-search-result"></div>
- </div>
- </div>
- </div>
- </div>
-
-
- </main>
- <footer>
- <div class="footer-inner">
-
- <div class="footer-content">
- <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/limour-blog.github.io" target="_blank" rel="nofollow noopener"><span>SRC</span></a> <i class="iconfont icon-love"></i> <a href="https://web.archive.org/web/20231130095837/https://effectiveacceleration.tech/" target="_blank" rel="nofollow noopener"><span>e/Acc</span></a>
- </div>
-
-
-
- </div>
- </footer>
- <!-- Scripts -->
-
- <script src="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.js" ></script>
- <link rel="stylesheet" href="https://jscdn.limour.top/npm/nprogress@0.2.0/nprogress.min.css" />
- <script>
- NProgress.configure({"showSpinner":false,"trickleSpeed":100})
- NProgress.start()
- window.addEventListener('load', function() {
- NProgress.done();
- })
- </script>
- <script src="https://jscdn.limour.top/npm/jquery@3.6.4/dist/jquery.min.js" ></script>
- <script src="https://jscdn.limour.top/npm/bootstrap@4.6.1/dist/js/bootstrap.min.js" ></script>
- <script src="/js/events.js" ></script>
- <script src="/js/plugins.js" ></script>
-
- <script src="/js/img-lazyload.js" ></script>
-
-
- <script>
- Fluid.utils.createScript('https://jscdn.limour.top/npm/tocbot@4.20.1/dist/tocbot.min.js', function() {
- var toc = jQuery('#toc');
- if (toc.length === 0 || !window.tocbot) { return; }
- var boardCtn = jQuery('#board-ctn');
- var boardTop = boardCtn.offset().top;
- window.tocbot.init(Object.assign({
- tocSelector : '#toc-body',
- contentSelector : '.markdown-body',
- linkClass : 'tocbot-link',
- activeLinkClass : 'tocbot-active-link',
- listClass : 'tocbot-list',
- isCollapsedClass: 'tocbot-is-collapsed',
- collapsibleClass: 'tocbot-is-collapsible',
- scrollSmooth : true,
- includeTitleTags: true,
- headingsOffset : -boardTop,
- }, CONFIG.toc));
- if (toc.find('.toc-list-item').length > 0) {
- toc.css('visibility', 'visible');
- }
- Fluid.events.registerRefreshCallback(function() {
- if ('tocbot' in window) {
- tocbot.refresh();
- var toc = jQuery('#toc');
- if (toc.length === 0 || !tocbot) {
- return;
- }
- if (toc.find('.toc-list-item').length > 0) {
- toc.css('visibility', 'visible');
- }
- }
- });
- });
- </script>
- <script src=https://lib.baomitu.com/clipboard.js/2.0.11/clipboard.min.js></script>
- <script>Fluid.plugins.codeWidget();</script>
-
- <script>
- Fluid.utils.createScript('https://jscdn.limour.top/npm/anchor-js@4.3.1/anchor.min.js', function() {
- window.anchors.options = {
- placement: CONFIG.anchorjs.placement,
- visible : CONFIG.anchorjs.visible
- };
- if (CONFIG.anchorjs.icon) {
- window.anchors.options.icon = CONFIG.anchorjs.icon;
- }
- var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
- var res = [];
- for (var item of el) {
- res.push('.markdown-body > ' + item.trim());
- }
- if (CONFIG.anchorjs.placement === 'left') {
- window.anchors.options.class = 'anchorjs-link-left';
- }
- window.anchors.add(res.join(', '));
- Fluid.events.registerRefreshCallback(function() {
- if ('anchors' in window) {
- anchors.removeAll();
- var el = (CONFIG.anchorjs.element || 'h1,h2,h3,h4,h5,h6').split(',');
- var res = [];
- for (var item of el) {
- res.push('.markdown-body > ' + item.trim());
- }
- if (CONFIG.anchorjs.placement === 'left') {
- anchors.options.class = 'anchorjs-link-left';
- }
- anchors.add(res.join(', '));
- }
- });
- });
- </script>
- <script>Fluid.plugins.imageCaption();</script>
- <script src="/js/local-search.js" ></script>
- <!-- 主题的启动项，将它保持在最底部 -->
- <!-- the boot of the theme, keep it at the bottom -->
- <script src="/js/boot.js" ></script>
-
- <noscript>
- <div class="noscript-warning">Blog works best with JavaScript enabled</div>
- </noscript>
- <!-- hexo injector body_end start -->
- <script defer src="/theme-inject/timeliness.js"></script>
- <!-- hexo injector body_end end --></body>
- </html>
|
