<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<meta name="description" content="Gene set score calculation.
">
<title>Gene set score calculation • SpaCET</title>
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="../deps/bootstrap-5.1.0/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.1.0/bootstrap.bundle.min.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Gene set score calculation">
<meta property="og:description" content="Gene set score calculation.
">
<!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
    

    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
    
    <a class="navbar-brand me-2" href="../index.html">SpaCET</a>

    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.2.0</small>

    
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
      <span class="navbar-toggler-icon"></span>
    </button>

    <div id="navbar" class="collapse navbar-collapse ms-3">
      <ul class="navbar-nav me-auto">
<li class="nav-item">
  <a class="nav-link" href="../index.html">
    <span class="fas fa fas fa-home fa-lg"></span>
     
  </a>
</li>
<li class="nav-item">
  <a class="nav-link" href="../reference/index.html">Reference</a>
</li>
<li class="active nav-item dropdown">
  <a href="#" class="nav-link dropdown-toggle" data-bs-toggle="dropdown" role="button" aria-expanded="false" aria-haspopup="true" id="dropdown-tutorials">Tutorials</a>
  <div class="dropdown-menu" aria-labelledby="dropdown-tutorials">
    <h6 class="dropdown-header" data-toc-skip>Core</h6>
    <a class="dropdown-item" href="../articles/visium_BC.html">Cell type deconvolution and interaction analysis</a>
    <a class="dropdown-item" href="../articles/oldST_PDAC.html">Deconvolution with a matched scRNA-seq data set</a>
    <div class="dropdown-divider"></div>
    <h6 class="dropdown-header" data-toc-skip>Misc</h6>
    <a class="dropdown-item" href="../articles/GeneSetScore.html">Gene set score calculation for spatial spots</a>
  </div>
</li>
<li class="nav-item">
  <a class="nav-link" href="../news/index.html">News</a>
</li>
      </ul>
<form class="form-inline my-2 my-lg-0" role="search">
        <input type="search" class="form-control me-sm-2" aria-label="Toggle navigation" name="search-input" data-search-index="../search.json" id="search-input" placeholder="Search for" autocomplete="off">
</form>

      <ul class="navbar-nav">
<li class="nav-item">
  <a class="external-link nav-link" href="https://github.com/data2intelligence/SpaCET/" aria-label="github">
    <span class="fab fa fab fa-github fa-lg"></span>
     
  </a>
</li>
      </ul>
</div>

    
  </div>
</nav><div class="container template-article">




<div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="" class="logo" alt=""><h1>Gene set score calculation</h1>
            
      
      <small class="dont-index">Source: <a href="https://github.com/data2intelligence/SpaCET/blob/HEAD/vignettes/GeneSetScore.Rmd" class="external-link"><code>vignettes/GeneSetScore.Rmd</code></a></small>
      <div class="d-none name"><code>GeneSetScore.Rmd</code></div>
    </div>

    
    
<p>In this vignette, we will demonstrate how to use <code>SpaCET</code>
to calculate and visualize spots’ gene set score for the in-house or
user-defined gene sets. The in-house gene sets include hallmarks, cancer
cell states, and tertiary lymphoid structures (TLS).</p>
<div class="section level2">
<h2 id="create-spacet-object">Create SpaCET object<a class="anchor" aria-label="anchor" href="#create-spacet-object"></a>
</h2>
<p>To read your ST data into R, user can create an SpaCET object by
using <code>create.SpaCET.object</code> or
<code>create.SpaCET.object.10X</code>. Specifically, if users are
analyzing an ST dataset from 10x Visium, they only need to input
“visiumPath” by using <code>create.SpaCET.object.10X</code>. Please make
sure that “visiumPath” points to the standard output folders of 10x
Space Ranger, which has both “filtered_feature_bc_matrix” and “spatial”
folders.</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/data2intelligence/SpaCET" class="external-link">SpaCET</a></span><span class="op">)</span></span>
<span></span>
<span><span class="co"># set the path to the in-house breast cancer ST data. User can set the paths to their own data.</span></span>
<span><span class="va">visiumPath</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/file.path.html" class="external-link">file.path</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/system.file.html" class="external-link">system.file</a></span><span class="op">(</span>package <span class="op">=</span> <span class="st">"SpaCET"</span><span class="op">)</span>, <span class="st">"extdata/Visium_BC"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># load ST data to create an SpaCET object.</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/create.SpaCET.object.10X.html">create.SpaCET.object.10X</a></span><span class="op">(</span>visiumPath <span class="op">=</span> <span class="va">visiumPath</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># calculate the QC metrics</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SpaCET.quality.control.html">SpaCET.quality.control</a></span><span class="op">(</span><span class="va">SpaCET_obj</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="calculate-hallmark-score">Calculate hallmark score<a class="anchor" aria-label="anchor" href="#calculate-hallmark-score"></a>
</h2>
<p>The in-house 50 hallmark gene sets were collected from <a href="https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#H" target="_blank" class="external-link">MSigDB</a> and user just need to set
<code>GeneSets</code> as “Hallmark”. <code>SpaCET.GeneSetScore</code>
will call <code>UCell</code> package to calculate gene set score. The
results are stored in <code>SpaCET_obj@results$GeneSetScore</code> as a
matrix.</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># run gene set calculation</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SpaCET.GeneSetScore.html">SpaCET.GeneSetScore</a></span><span class="op">(</span><span class="va">SpaCET_obj</span>, GeneSets<span class="op">=</span><span class="st">"Hallmark"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># show results</span></span>
<span><span class="va">SpaCET_obj</span><span class="op">@</span><span class="va">results</span><span class="op">$</span><span class="va">GeneSetScore</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">6</span>,<span class="fl">1</span><span class="op">:</span><span class="fl">6</span><span class="op">]</span></span>
<span></span>
<span><span class="co"># show all gene sets</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">SpaCET_obj</span><span class="op">@</span><span class="va">results</span><span class="op">$</span><span class="va">GeneSetScore</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># visualize two gene sets</span></span>
<span><span class="fu"><a href="../reference/SpaCET.visualize.spatialFeature.html">SpaCET.visualize.spatialFeature</a></span><span class="op">(</span></span>
<span>  <span class="va">SpaCET_obj</span>, </span>
<span>  spatialType <span class="op">=</span> <span class="st">"GeneSetScore"</span>, </span>
<span>  spatialFeatures <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"HALLMARK_HYPOXIA"</span>,<span class="st">"HALLMARK_TGF_BETA_SIGNALING"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p><img src="img/GS1.png" width="100%" style="border:none"></p>
</div>
<div class="section level2">
<h2 id="calculate-cancer-cell-state-score">Calculate cancer cell state score<a class="anchor" aria-label="anchor" href="#calculate-cancer-cell-state-score"></a>
</h2>
<p>A recent <a href="https://www.nature.com/articles/s41588-022-01141-9" target="_blank" class="external-link">study</a> identifies a catalog of gene modules whose
expression defines 16 recurrent cancer cell states through a pan-caner
single-cell RNA-sequencing analysis. In order to use them, user just
need to set <code>GeneSets</code> as “CancerCellState”.</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># run gene set calculation</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SpaCET.GeneSetScore.html">SpaCET.GeneSetScore</a></span><span class="op">(</span><span class="va">SpaCET_obj</span>, GeneSets<span class="op">=</span><span class="st">"CancerCellState"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># show all gene sets</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">rownames</a></span><span class="op">(</span><span class="va">SpaCET_obj</span><span class="op">@</span><span class="va">results</span><span class="op">$</span><span class="va">GeneSetScore</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># visualize two gene sets</span></span>
<span><span class="fu"><a href="../reference/SpaCET.visualize.spatialFeature.html">SpaCET.visualize.spatialFeature</a></span><span class="op">(</span></span>
<span>  <span class="va">SpaCET_obj</span>, </span>
<span>  spatialType <span class="op">=</span> <span class="st">"GeneSetScore"</span>, </span>
<span>  spatialFeatures <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CancerCellState_Cycle"</span>,<span class="st">"CancerCellState_cEMT"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p><img src="img/GS2.png" width="100%" style="border:none"></p>
</div>
<div class="section level2">
<h2 id="calculate-tls-score">Calculate TLS score<a class="anchor" aria-label="anchor" href="#calculate-tls-score"></a>
</h2>
<p>User just need to set <code>GeneSets</code> as “TLS” to calculate
tertiary lymphoid structure score. We collected a 30-gene TLS signature
from this <a href="https://www.researchsquare.com/article/rs-3921508" target="_blank" class="external-link">study</a>.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># run gene set calculation</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SpaCET.GeneSetScore.html">SpaCET.GeneSetScore</a></span><span class="op">(</span><span class="va">SpaCET_obj</span>, GeneSets<span class="op">=</span><span class="st">"TLS"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># visualize TLS</span></span>
<span><span class="fu"><a href="../reference/SpaCET.visualize.spatialFeature.html">SpaCET.visualize.spatialFeature</a></span><span class="op">(</span></span>
<span>  <span class="va">SpaCET_obj</span>, </span>
<span>  spatialType <span class="op">=</span> <span class="st">"GeneSetScore"</span>, </span>
<span>  spatialFeatures <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TLS"</span><span class="op">)</span></span>
<span><span class="op">)</span></span></code></pre></div>
<p><img src="img/GS3.png" width="50%" style="border:none"></p>
</div>
<div class="section level2">
<h2 id="calculate-other-gene-sets-score">Calculate other gene sets’ score<a class="anchor" aria-label="anchor" href="#calculate-other-gene-sets-score"></a>
</h2>
<p>There are two methods to build customized gene sets. 1) Generate a
list to define some simple gene sets (e.g., T cell and Myeloid
signatures). 2) Download a gmt file from <a href="https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp" target="_blank" class="external-link">MSigDB</a> (e.g., GO Ontology), and then use
<code>read.gmt</code> to read this file as a list.</p>
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># 1)</span></span>
<span><span class="va">gmt1</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span>
<span>  Tcell <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"CD2"</span>,<span class="st">"CD3E"</span>,<span class="st">"CD3D"</span><span class="op">)</span>, </span>
<span>  Myeloid <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"SPI1"</span>,<span class="st">"FCER1G"</span>,<span class="st">"CSF1R"</span><span class="op">)</span></span>
<span><span class="op">)</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SpaCET.GeneSetScore.html">SpaCET.GeneSetScore</a></span><span class="op">(</span><span class="va">SpaCET_obj</span>, GeneSets <span class="op">=</span> <span class="va">gmt1</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># 2)</span></span>
<span><span class="va">gmt2</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/read.gmt.html">read.gmt</a></span><span class="op">(</span><span class="st">"Path_to_gmt_file"</span><span class="op">)</span></span>
<span><span class="va">SpaCET_obj</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/SpaCET.GeneSetScore.html">SpaCET.GeneSetScore</a></span><span class="op">(</span><span class="va">SpaCET_obj</span>, GeneSets <span class="op">=</span> <span class="va">gmt2</span><span class="op">)</span></span></code></pre></div>
</div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
    </nav></aside>
</div>



    <footer><div class="pkgdown-footer-left">
  <p></p>
<p>Developed by Beibei Ru, Peng Jiang.</p>
</div>

<div class="pkgdown-footer-right">
  <p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

    </footer>
</div>

  

  

  </body>
</html>
