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<div>
(This article was first published on <strong><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree"> R on Guangchuang YU</a></strong>, and kindly contributed to <a rel="nofollow" href="https://www.r-bloggers.com/">R-bloggers)</a> </div>
<p><a target="_blank" href="https://guangchuangyu.github.io/ggtree">ggtree</a> provides many helper functions for manupulating phylogenetic trees and make it easy to explore tree structure visually.</p>
<p>Here, as examples, I used <code>ggtree</code> to draw capital character <code>G</code> and <code>C</code>, which are first letter of my name :-).</p>
<p>To draw a tree in such shape, we need <code>fan</code> layout (<code>circular</code> layout with open angle) and then rotating the tree to let the open space on the correct position. Here are the source codes to produce the <code>G</code> and <code>C</code> shapes of tree. I am thinking about using the <code>G</code> shaped tree as <code>ggtree</code> logo. Have fun with <code>ggtree</code> <img alt="🙂" class="wp-smiley" src="https://s.w.org/images/core/emoji/72x72/1f642.png"></p>
<pre><code>library(ggtree)

beast_file &lt;- system.file(&quot;examples/MCC_FluA_H3.tree&quot;, package=&quot;ggtree&quot;)
beast_tree &lt;- read.beast(beast_file)

genotype_file &lt;- system.file(&quot;examples/Genotype.txt&quot;, package=&quot;ggtree&quot;)
genotype &lt;- read.table(genotype_file, sep=&quot;\t&quot;, stringsAsFactor=F)
p &lt;- ggtree(beast_tree, layout='circular', color=&quot;#4DAF4A&quot;, size=2, branch.length='none', right=T) +
    annotate('text', x=0, y=40, label='ggtree', family='mono', size=16)

p2 &lt;- gheatmap(p, genotype, width=0.2, hjust='left', colnames_angle=-10, font.size=1.5)  +
    scale_fill_manual(values=c(&quot;#E41A1C&quot;,&quot;#377EB8&quot;,&quot;#FC8D59&quot;)) + theme_tree()

open_tree(p2, 80) %>% rotate_tree(80)
</code></pre>
<p><img alt="" src="https://i1.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/ggtree/logoG.png?w=456&ssl=1" data-recalc-dims="1"></p>
<pre><code>p &lt;- ggtree(beast_tree, layout='circular', color=&quot;#4DAF4A&quot;, 
           size=2, branch.length='none', right=T) + xlim(-30, NA)
p2 &lt;- gheatmap(p, genotype, width=0.2, hjust='left', colnames=F) +
    scale_fill_manual(values=c(&quot;#E41A1C&quot;,&quot;#377EB8&quot;,&quot;#FC8D59&quot;)) + theme_tree()

open_tree(p2, 90) %>% rotate_tree(50)
</code></pre>
<p><img alt="" src="https://i0.wp.com/guangchuangyu.github.io/blog_images/Bioconductor/ggtree/logoC.png?w=456&ssl=1" data-recalc-dims="1"></p>
<h2>Citation</h2>
<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. <a target="_blank" href="http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a>. <strong><em>Methods in Ecology and Evolution</em></strong>. <a target="_blank" href="http://dx.doi.org/10.1111/2041-210X.12628"><code>doi:10.1111/2041-210X.12628</code></a>.</p>
<p></p>
<div data-badge-popover="right" data-doi="10.1111/2041-210X.12628" data-badge-type="donut"></div>
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