<!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>BioCartaImage • BioCartaImage</title><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></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="BioCartaImage"><!-- 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-title-body">
<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">BioCartaImage</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.99.0</span>
</span>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav"><li>
<a href="articles/BioCartaImage.html">Get started</a>
</li>
<li>
<a href="reference/index.html">Reference</a>
</li>
</ul><ul class="nav navbar-nav navbar-right"><li>
<a href="https://github.com/jokergoo/BioCartaImage/" class="external-link">
<span class="fab fa-github fa-lg"></span>
</a>
</li>
</ul></div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
</header><div class="row">
<div class="contents col-md-9">
<div class="page-header">
<h1>BioCartaImage</h1>
</div>
<div id="biocartaimage" class="section level1">
<p>BioCarta is a valuable source of biological pathways which not only provides well manually curated pathways, but also remarkably intuitive pathway images. One useful features of pathway analysis which is to highlight genes of interest on the pathway images has been lost. Since the original source of BioCarta (biocarte.com) is lost from the internet, we digged out the data from the internet archive and formatted it into a package.</p>
<div class="section level2">
<h2 id="install">Install<a class="anchor" aria-label="anchor" href="#install"></a></h2>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu">devtools</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"jokergoo/BioCartaImage"</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a></h2>
<div class="sourceCode" id="cb2"><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/jokergoo/BioCartaImage" class="external-link">BioCartaImage</a></span><span class="op">)</span></span>
<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">grid</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/grid/grid.newpage.html" class="external-link">grid.newpage</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="fu"><a href="reference/pathwayGrob.html">grid.pathway</a></span><span class="op">(</span><span class="st">"h_RELAPathway"</span><span class="op">)</span></span></code></pre></div>
<div class="figure">
<img src="https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38/assets/449218/ffc692c2-729f-41cf-a045-bf28168a39c6" alt=""><p class="caption">image</p>
</div>
<p>Highlight genes:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/grid/grid.newpage.html" class="external-link">grid.newpage</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="fu"><a href="reference/pathwayGrob.html">grid.pathway</a></span><span class="op">(</span><span class="st">"h_RELAPathway"</span>, color <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">"1387"</span> <span class="op">=</span> <span class="st">"yellow"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<div class="figure">
<img src="https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38/assets/449218/89f3a5d6-3b14-4e6c-a4b4-f7469dbb6528" alt=""><p class="caption">image</p>
</div>
<p>Add advanced graphics:</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">grob</span> <span class="op">=</span> <span class="fu"><a href="reference/pathwayGrob.html">pathwayGrob</a></span><span class="op">(</span><span class="st">"h_RELAPathway"</span><span class="op">)</span></span>
<span></span>
<span><span class="fu"><a href="https://rdrr.io/r/grid/grid.newpage.html" class="external-link">grid.newpage</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="va">grob4</span> <span class="op">=</span> <span class="fu"><a href="reference/mark_gene.html">mark_gene</a></span><span class="op">(</span><span class="va">grob</span>, <span class="st">"1387"</span>, <span class="kw">function</span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="va">pos</span> <span class="op">=</span> <span class="fu"><a href="reference/pos_by_polygon.html">pos_by_polygon</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/grid/viewports.html" class="external-link">pushViewport</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/grid/viewport.html" class="external-link">viewport</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">pos</span><span class="op">[</span><span class="fl">1</span><span class="op">]</span> <span class="op">-</span> <span class="fl">10</span>, y <span class="op">=</span> <span class="va">pos</span><span class="op">[</span><span class="fl">2</span><span class="op">]</span>, </span>
<span> width <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/grid/unit.html" class="external-link">unit</a></span><span class="op">(</span><span class="fl">4</span>, <span class="st">"cm"</span><span class="op">)</span>, height <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/grid/unit.html" class="external-link">unit</a></span><span class="op">(</span><span class="fl">4</span>, <span class="st">"cm"</span><span class="op">)</span>, </span>
<span> default.units <span class="op">=</span> <span class="st">"native"</span>, just <span class="op">=</span> <span class="st">"right"</span><span class="op">)</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/grid/grid.rect.html" class="external-link">grid.rect</a></span><span class="op">(</span>gp <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/grid/gpar.html" class="external-link">gpar</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="st">"red"</span><span class="op">)</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/grid/grid.text.html" class="external-link">grid.text</a></span><span class="op">(</span><span class="st">"add whatever\nyou want here"</span><span class="op">)</span></span>
<span> <span class="fu"><a href="https://rdrr.io/r/grid/viewports.html" class="external-link">popViewport</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="op">}</span>, capture <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/grid/grid.draw.html" class="external-link">grid.draw</a></span><span class="op">(</span><span class="va">grob4</span><span class="op">)</span></span></code></pre></div>
<div class="figure">
<img src="https://github.com/jokergoo/IlluminaHumanMethylationEPICv2anno.20a1.hg38/assets/449218/cef41abf-ec39-4384-9e51-3e3c809ebac0" alt=""><p class="caption">image</p>
</div>
</div>
<div class="section level2">
<h2 id="license">License<a class="anchor" aria-label="anchor" href="#license"></a></h2>
<p>MIT @ Zuguang Gu</p>
</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 Zuguang Gu.</p>
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>
</footer></div>
</body></html>
