<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="author" content="Guangchuang Yu">
<link rel="canonical" href="https://guangchuangyu.github.io/ggtree/">
<link rel="shortcut icon" href="./img/favicon.ico">
<title>ggtree</title>
<link href="./css/bootstrap-custom.min.css" rel="stylesheet">
<link href="./css/font-awesome-4.0.3.css" rel="stylesheet">
<link rel="stylesheet" href="./css/highlight.css">
<link href="./css/base.css" rel="stylesheet">
<!-- HTML5 shim and Respond.js IE8 support of HTML5 elements and media queries -->
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/libs/html5shiv/3.7.0/html5shiv.js"></script>
<script src="https://oss.maxcdn.com/libs/respond.js/1.3.0/respond.min.js"></script>
<![endif]-->
<script>
(function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
(i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
})(window,document,'script','//www.google-analytics.com/analytics.js','ga');
ga('create', 'UA-77901140-1', 'guangchuangyu.github.io');
ga('send', 'pageview');
</script>
</head>
<body>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<!-- Collapsed navigation -->
<div class="navbar-header">
<!-- Expander button -->
<button type="button" class="navbar-toggle" data-toggle="collapse" data-target=".navbar-collapse">
<span class="sr-only">Toggle navigation</span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<!-- Main title -->
<a class="navbar-brand" href=".">ggtree</a>
</div>
<!-- Expanded navigation -->
<div class="navbar-collapse collapse">
<!-- Main navigation -->
<ul class="nav navbar-nav">
<li class="active">
<a href=".">Home</a>
</li>
<li >
<a href="documentation/">Documentation</a>
</li>
<li >
<a href="faq/">FAQ</a>
</li>
<li >
<a href="featuredArticles/">Featured Articles</a>
</li>
<li >
<a href="gallery/">Gallery</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown">Software <b class="caret"></b></a>
<ul class="dropdown-menu">
<li >
<a href="ChIPseeker/">ChIPseeker</a>
</li>
<li >
<a href="clusterProfiler/">clusterProfiler</a>
</li>
<li >
<a href="DOSE/">DOSE</a>
</li>
<li >
<a href="emojifont/">emojifont</a>
</li>
<li >
<a href="ggtree/">ggtree</a>
</li>
<li >
<a href="GOSemSim/">GOSemSim</a>
</li>
<li >
<a href="meshes/">meshes</a>
</li>
<li >
<a href="ReactomePA/">ReactomePA</a>
</li>
<li >
<a href="treeio/">treeio</a>
</li>
</ul>
</li>
</ul>
<!-- Search, Navigation and Repo links -->
<ul class="nav navbar-nav navbar-right">
<li>
<a href="#" data-toggle="modal" data-target="#mkdocs_search_modal">
<i class="fa fa-search"></i> Search
</a>
</li>
<li class="disabled">
<a rel="next" >
<i class="fa fa-arrow-left"></i> Previous
</a>
</li>
<li >
<a rel="prev" href="documentation/">
Next <i class="fa fa-arrow-right"></i>
</a>
</li>
<li>
<a href="https://github.com/GuangchuangYu/ggtree">
<i class="fa fa-github"></i>
GitHub
</a>
</li>
</ul>
</div>
</div>
</div>
<div class="container">
<div class="col-md-3"><div class="bs-sidebar hidden-print affix well" role="complementary">
<ul class="nav bs-sidenav">
<li class="main active"><a href="#ggtree-visualization-and-annotation-of-phylogenetic-trees">ggtree: visualization and annotation of phylogenetic trees</a></li>
<li><a href="#authors"> Authors</a></li>
<li><a href="#citation"> Citation</a></li>
<li><a href="#featured-articles"> Featured Articles</a></li>
<li><a href="#installation"> Installation</a></li>
<li><a href="#overview"> Overview</a></li>
<li><a href="#projects-that-depend-on-ggtree"> Projects that depend on ggtree</a></li>
<li><a href="#feedback"> Feedback</a></li>
</ul>
</div></div>
<div class="col-md-9" role="main">
<h1 id="ggtree-visualization-and-annotation-of-phylogenetic-trees">ggtree: visualization and annotation of phylogenetic trees</h1>
<!-- AddToAny BEGIN -->
<div class="a2a_kit a2a_kit_size_32 a2a_default_style">
<a class="a2a_dd" href="//www.addtoany.com/share"></a>
<a class="a2a_button_facebook"></a> <a class="a2a_button_twitter"></a>
<a class="a2a_button_google_plus"></a>
<a class="a2a_button_pinterest"></a> <a class="a2a_button_reddit"></a>
<a class="a2a_button_sina_weibo"></a> <a class="a2a_button_wechat"></a>
<a class="a2a_button_douban"></a>
</div>
<script async src="//static.addtoany.com/menu/page.js"></script>
<!-- AddToAny END -->
<p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
<link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
<p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a>
<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.2-blue.svg?style=flat" /></a>
<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-17163/total-blue.svg?style=flat" /></a>
<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
<p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>
is designed for not only viewing phylogenetic tree but also displaying
annotation data on the tree. <em>ggtree</em> is released within the
<a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and
the source code is hosted on
<a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i>
GitHub</a>.</p>
<h2 id="authors"><i class="fa fa-user"></i> Authors</h2>
<p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The
University of Hong Kong.</p>
<p><a href="https://twitter.com/guangchuangyu"><i class="fa fa-twitter fa-3x"></i></a>
<a href="https://guangchuangyu.github.io/blog_images/biobabble.jpg"><i class="fa fa-wechat fa-3x"></i></a>
<a href="https://www.ncbi.nlm.nih.gov/pubmed/?term=Guangchuang+Yu[Author+-+Full]"><i class="ai ai-pubmed ai-3x"></i></a>
<a href="https://scholar.google.com.hk/citations?user=DO5oG40AAAAJ&hl=en"><i class="ai ai-google-scholar ai-3x"></i></a>
<a href="https://orcid.org/0000-0002-6485-8781"><i class="ai ai-orcid ai-3x"></i></a>
<a href="https://impactstory.org/u/0000-0002-6485-8781"><i class="ai ai-impactstory ai-3x"></i></a></p>
<h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
<p>Please cite the following article when using <code>ggtree</code>:</p>
<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat" /></a>
<a href="https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-26-blue.svg?style=flat" /></a></p>
<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R
package for visualization and annotation of phylogenetic trees with
their covariates and other associated data. <strong><em>Methods in Ecology and
Evolution</em></strong>. 2017, 8(1):28-36.</p>
<h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
<p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
<p><i class="fa fa-hand-o-right"></i> Find out more on
<i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/ggtree/featuredArticles/">Featured
Articles</a>.</p>
<h2 id="installation"><i class="fa fa-download"></i> Installation</h2>
<p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor
page</a>:</p>
<pre><code class="r">## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
## biocLite("BiocUpgrade") ## you may need this
biocLite("ggtree")
</code></pre>
<p>If you have problems when installing some of the dependent packages,
please refer to the
<a href="https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation">ggtree-installation</a>
wiki page.</p>
<h2 id="overview"><i class="fa fa-cogs"></i> Overview</h2>
<h4 id="getting-tree-into-r"><i class="fa fa-angle-double-right"></i> Getting tree into R</h4>
<ul>
<li>tree parsers: bring evolution evidences to be used/analyzed in <code>R</code></li>
<li><code>merge_tree</code>: allows evolution evidences to be merged and compared</li>
<li><code>fortify</code> methods: convert tree objects into tidy data frame</li>
</ul>
<h4 id="tree-visualization-annotation"><i class="fa fa-angle-double-right"></i> Tree visualization & annotation</h4>
<ul>
<li>parsing tree as a collection of nodes allows grammar of graphics to
be supported</li>
<li><code>geom_tree</code>: extends <code>ggplot2</code> to support tree structure</li>
<li>several layers and functions for tree annotation</li>
<li>supports annotating phylogenetic trees with user's own data</li>
</ul>
<h4 id="tree-manipulation"><i class="fa fa-angle-double-right"></i> Tree manipulation</h4>
<ul>
<li>helper functions for tree manipulation, make it possible to explore
the tree visually</li>
</ul>
<p><i class="fa fa-hand-o-right"></i> Find out details and examples on
<i class="fa fa-book"></i>
<a href="https://guangchuangyu.github.io/ggtree/documentation/">Documentation</a>.</p>
<h2 id="projects-that-depend-on-ggtree"><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>
<h4 id="cran-packages"><i class="fa fa-angle-double-right"></i> CRAN packages</h4>
<ul>
<li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle
Phylogenetic Distance Matrices and Other Utilities</li>
</ul>
<h4 id="bioconductor-packages"><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
<ul>
<li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of
lincRNAs and protein-coding genes</li>
<li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>:
Analyze high-throughput sequencing of T and B cell receptors</li>
<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic
partitioning based ILR transform for metagenomics data</li>
</ul>
<h4 id="other-applications"><i class="fa fa-angle-double-right"></i> Other applications</h4>
<ul>
<li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>:
Collection of scripts for metagenomics analysis</li>
<li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>:
Utilities for Creating and Validating Degenerate primers</li>
<li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies
created along a genome for patterns</li>
</ul>
<h2 id="feedback"><i class="fa fa-comments"></i> Feedback</h2>
<ul class="fa-ul">
<li><i class="fa-li fa fa-hand-o-right"></i> Please make sure you have followed <a href="https://guangchuangyu.github.io/2016/07/how-to-bug-author/"><strong>the important guide</strong></a> before posting any issue/question</li>
<li><i class="fa-li fa fa-bug"></i> For bugs or feature requests, please post to <i class="fa fa-github-alt"></i> <a href="https://github.com/GuangchuangYu/ggtree/issues">github issue</a></li>
<li><i class="fa-li fa fa-question"></i> For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>
<li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a></li>
<li><i class="fa-li fa fa-commenting"></i> Join the group chat on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a></li>
</ul></div>
</div>
<footer class="col-md-12">
<hr>
<center>Copyright © 2016 <a href="https://guangchuangyu.github.io">Guangchuang Yu</a>.<div style="width:250px;margin:auto;"><script type="text/javascript" src="//rf.revolvermaps.com/0/0/7.js?i=5qpvv5zz7fp&m=0&c=ff0000&cr1=ffffff&sx=0" async="async"></script></div></center>
<center>Documentation built with <a href="http://www.mkdocs.org/">MkDocs</a>.</center>
</footer>
<script src="./js/jquery-1.10.2.min.js"></script>
<script src="./js/bootstrap-3.0.3.min.js"></script>
<script src="./js/highlight.pack.js"></script>
<script>var base_url = '.';</script>
<script data-main="./mkdocs/js/search.js" src="./mkdocs/js/require.js"></script>
<script src="./js/base.js"></script>
<div class="modal" id="mkdocs_search_modal" tabindex="-1" role="dialog" aria-labelledby="Search Modal" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<button type="button" class="close" data-dismiss="modal"><span aria-hidden="true">×</span><span class="sr-only">Close</span></button>
<h4 class="modal-title" id="exampleModalLabel">Search</h4>
</div>
<div class="modal-body">
<p>
From here you can search these documents. Enter
your search terms below.
</p>
<form role="form">
<div class="form-group">
<input type="text" class="form-control" placeholder="Search..." id="mkdocs-search-query">
</div>
</form>
<div id="mkdocs-search-results"></div>
</div>
<div class="modal-footer">
</div>
</div>
</div>
</div>
</body>
</html>
