<!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=1.0"><title>Proportion of features — feature_percent • SeuratExtend</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.7.1/jquery.min.js" integrity="sha512-v2CJ7UaYy4JwqLDIrZUI/4hqeoQieOmAZNXBeQyjo21dadnwR+8ZaIJVT8EE2iyI61OV8e6M8PP2/4hpQINQ/g==" crossorigin="anonymous" referrerpolicy="no-referrer"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.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"><!-- 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><!-- 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><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><meta property="og:title" content="Proportion of features — feature_percent"><meta property="og:description" content="Check the Proportion of positive cells (default: expression above 0)
in certain clusters"><!-- 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 data-spy="scroll" data-target="#toc">
    

    <div class="container template-reference-topic">
      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">SeuratExtend</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">1.0.0</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../reference/index.html">Reference</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"></ul></div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>Proportion of features</h1>
    
    <div class="hidden name"><code>feature_percent.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>Check the Proportion of positive cells (default: expression above 0)
in certain clusters</p>
    </div>

    <div id="ref-usage">
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">feature_percent</span><span class="op">(</span></span>
<span>  <span class="va">seu</span>,</span>
<span>  <span class="va">feature</span>,</span>
<span>  ident <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  group.by <span class="op">=</span> <span class="cn">NULL</span>,</span>
<span>  DefaultAssay <span class="op">=</span> <span class="st">"RNA"</span>,</span>
<span>  above <span class="op">=</span> <span class="fl">0</span>,</span>
<span>  total <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  if.expressed <span class="op">=</span> <span class="cn">F</span>,</span>
<span>  min.pct <span class="op">=</span> <span class="fl">0.1</span></span>
<span><span class="op">)</span></span></code></pre></div>
    </div>

    <div id="arguments">
    <h2>Arguments</h2>
    <dl><dt>seu</dt>
<dd><p>Seurat object</p></dd>


<dt>feature</dt>
<dd><p>Features to plot (gene expression, metrics, PC scores, anything that can be
retreived by FetchData)</p></dd>


<dt>ident</dt>
<dd><p>cluster name, Default: all clusters</p></dd>


<dt>group.by</dt>
<dd><p>A variable name in meta.data to group by, if you don't want to use
default Idents of Seurat object</p></dd>


<dt>DefaultAssay</dt>
<dd><p>Assay to use, Default: 'RNA'</p></dd>


<dt>above</dt>
<dd><p>Above which value will be considered as positive cell, Default: 0</p></dd>


<dt>total</dt>
<dd><p>If to calculate proportion in total cells of selected clusters, Default: F</p></dd>


<dt>if.expressed</dt>
<dd><p>If only return logical value, Default: F</p></dd>


<dt>min.pct</dt>
<dd><p>Minimum fraction of min.pct cells in the cluster will be considered "expressed",
only use this parameter when "if.expressed" is set to TRUE. Default: 0.1</p></dd>

</dl></div>
    <div id="value">
    <h2>Value</h2>
    

<p>A matrix</p>
    </div>
    <div id="details">
    <h2>Details</h2>
    <p>None.</p>
    </div>

    <div id="ref-examples">
    <h2>Examples</h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="va">genes</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://mojaveazure.github.io/seurat-object/reference/VariableFeatures.html" class="external-link">VariableFeatures</a></span><span class="op">(</span><span class="va">pbmc</span><span class="op">)</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span></span>
<span></span>
<span><span class="fu">feature_percent</span><span class="op">(</span><span class="va">pbmc</span>, feature <span class="op">=</span> <span class="va">genes</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Count one cell as positive only the expression is above 2</span></span>
<span><span class="fu">feature_percent</span><span class="op">(</span><span class="va">pbmc</span>, feature <span class="op">=</span> <span class="va">genes</span>, above <span class="op">=</span> <span class="fl">2</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Only check subset of clusters</span></span>
<span><span class="fu">feature_percent</span><span class="op">(</span><span class="va">pbmc</span>, feature <span class="op">=</span> <span class="va">genes</span>, ident <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">"B cell"</span>, <span class="st">"CD8 T cell"</span><span class="op">)</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Group by a different variable</span></span>
<span><span class="fu">feature_percent</span><span class="op">(</span><span class="va">pbmc</span>, feature <span class="op">=</span> <span class="va">genes</span>, group.by <span class="op">=</span> <span class="st">"orig.ident"</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Also check the proportion of expressed cells in total clusters</span></span>
<span><span class="fu">feature_percent</span><span class="op">(</span><span class="va">pbmc</span>, feature <span class="op">=</span> <span class="va">genes</span>, total <span class="op">=</span> <span class="cn">T</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># only show logical value; 'TRUE' if more than 20% cells are positive</span></span>
<span><span class="fu">feature_percent</span><span class="op">(</span><span class="va">pbmc</span>, feature <span class="op">=</span> <span class="va">genes</span>, if.expressed <span class="op">=</span> <span class="cn">T</span>, min.pct <span class="op">=</span> <span class="fl">0.2</span><span class="op">)</span></span>
<span></span></code></pre></div>
    </div>
  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
    </nav></div>
</div>


      <footer><div class="copyright">
  <p></p><p>Developed by Yichao Hua.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.9.</p>
</div>

      </footer></div>

  


  

  </body></html>

