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<h3 class="navbar-left"><strong>ggplot2</strong> extensions</h3>

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ggplot2 now has an official extension mechanism. This means that others can now easily create their own stats, geoms and positions, and provide them in other packages. This should allow the ggplot2 community to flourish, even as less development work happens in ggplot2 itself. This page showcases these extensions.

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<h3>ggtree</h3>

<p><a href="https://bioconductor.org/packages/release/bioc/html/ggtree.html" class="uri">https://bioconductor.org/packages/release/bioc/html/ggtree.html</a></p>

<p>gtree is designed for visualizing phylogenetic tree and different types of associated annotation data.</p>

<pre class="r"><code># Example from https://bioconductor.org/packages/release/bioc/html/ggtree.html

library(ggplot2)

library(ape)

library(ggtree)</code></pre>

<div id="tree-data-import" class="section level4">

<h4>Tree Data Import</h4>

<pre class="r"><code>file &lt;- system.file(&quot;extdata/BEAST&quot;, &quot;beast_mcc.tree&quot;, package=&quot;ggtree&quot;)

beast &lt;- read.beast(file)</code></pre>

<p>Users can use <code>ggtree(beast)</code> to visualize the tree and add layer to annotate it.</p>

<pre class="r"><code>ggtree(beast, ndigits=2, branch.length = &#39;none&#39;) + geom_text(aes(x=branch, label=length_0.95_HPD), vjust=-.5, color=&#39;firebrick&#39;)</code></pre>

<p><img src="ggtree_files/figure-html/unnamed-chunk-3-1.png" title="" alt="" width="960" /></p>

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<div id="tree-visualization" class="section level4">

<h4>Tree Visualization</h4>

<p>To view a phylogenetic tree, we first need to parse the tree file into <code>R</code>. The <code>ggtree</code> package supports many file format including output files of commonly used software packages in evolutionary biology. For more details, plase refer to the <a href="treeImport.html">Tree Data Import</a> vignette.</p>

<pre class="r"><code>library(&quot;ggtree&quot;)

nwk &lt;- system.file(&quot;extdata&quot;, &quot;sample.nwk&quot;, package=&quot;ggtree&quot;)

tree &lt;- read.tree(nwk)

ggplot(tree, aes(x, y)) + geom_tree() + theme_tree()</code></pre>

<p><img src="ggtree_files/figure-html/unnamed-chunk-4-1.png" title="" alt="" width="576" /></p>

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<div id="tree-manipulation" class="section level4">

<h4>Tree Manipulation</h4>

<div id="internal-node-number" class="section level6">

<h6>Internal node number</h6>

<p>Some of the functions in <code>ggtree</code> works with clade and accepts a parameter of internal node number. To get the internal node number, user can use <code>geom_text2</code> to display it:</p>

<pre class="r"><code>nwk &lt;- system.file(&quot;extdata&quot;, &quot;sample.nwk&quot;, package=&quot;ggtree&quot;)

tree &lt;- read.tree(nwk)

ggtree(tree) + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) + geom_tiplab()</code></pre>

<p><img src="ggtree_files/figure-html/unnamed-chunk-5-1.png" title="" alt="" width="576" /></p>

<p>The following example use <code>groupOTU</code> to display taxa classification.</p>

<pre class="r"><code>data(chiroptera)

groupInfo &lt;- split(chiroptera$tip.label, gsub(&quot;_\\w+&quot;, &quot;&quot;, chiroptera$tip.label))

chiroptera &lt;- groupOTU(chiroptera, groupInfo)

ggtree(chiroptera, aes(color=group), layout=&#39;circular&#39;) + geom_tiplab(size=1, aes(angle=angle))</code></pre>

<p><img src="ggtree_files/figure-html/unnamed-chunk-6-1.png" title="" alt="" width="1344" /></p>

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