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plea to against bmc

guangchuang yu authored on 16/11/2017 03:28:27
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-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">
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-              Contact via email
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-            </a>
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+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">
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           </li>
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         </ul>
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+        <center><span class="zaln"><a href="https://guangchuangyu.github.io/2017/11/bmc-journal-protects-paper-of-plagiarism/" class="zb">Plea to against BMC</a></span></center>
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         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>
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 			<h1>Documentation </h1>
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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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-<div id="vignettes" class="section level2">
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 <h2><i class="fa fa-book"></i> Vignettes</h2>
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 <ul>
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 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>
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 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree utilities</a></li>
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 <li><a href="https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html">Phylomoji</a></li>
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 </ul>
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-<div id="blog-posts" class="section level2">
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 <h2><i class="fa fa-wordpress"></i> Blog posts</h2>
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-<div id="news-and-updates" class="section level3">
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 <h3><i class="fa fa-angle-double-right"></i> News and updates</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>
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 </ul>
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-<div id="data-manipulation" class="section level3">
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 <h3><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>
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 <li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>
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 </ul>
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-<div id="tree-visualization" class="section level3">
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 <h3><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
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 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
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 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
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 </ul>
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-<div id="tree-annotation" class="section level3">
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 <h3><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Application</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
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 <li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>
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 </ul>
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 <h2><i class="fa fa-slideshare"></i> Slides</h2>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>
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 <li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>
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 </ul>
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 <h2><i class="fa fa-youtube-play"></i> Video</h2>
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 <ul>
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 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
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 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
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 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
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 </ul>
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 <h2><i class="fa fa-gift"></i> Workflow</h2>
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 <li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>
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 			<aside class="copyright" role="note">
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-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">
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-              Contact via email
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-            </a>
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           </li>
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         </ul>
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+        <center><span class="zaln"><a href="https://guangchuangyu.github.io/2017/11/bmc-journal-protects-paper-of-plagiarism/" class="zb">Plea to against BMC</a></span></center>
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         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>
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 			<h1>FAQ </h1>
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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <h1><i class="fa fa-download"></i> Installation</h1>
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 <h2><i class="fa fa-angle-double-right"></i> Could not find function</h2>
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 <p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this error</a>, please make sure you are using the latest R and <code>ggtree</code>.</p>
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 <p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to <code>devel</code> branch.</p>
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 <p>Sometimes I may write blog post to introduce new functions which is not available in <code>release</code> branch, you need to install the <code>devel</code> version of <code>ggtree</code> in order to use these new functions.</p>
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 <p>You can download the <code>devel</code> version of <code>ggtree</code> from <a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html" class="uri">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and install it, or install the github version of <code>ggtree</code>.</p>
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 <p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>, <code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the <code>could not find function</code> error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.</p>
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 <h1><i class="fa fa-text-height"></i> Text &amp; Label</h1>
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 <h2><i class="fa fa-angle-double-right"></i> Tip label truncated</h2>
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 <p>ggplot2 can’t auto adjust xlim based on added text.</p>
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 <pre class="r"><code>library(ggtree)
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 ggtree(tree) + geom_tiplab()</code></pre>
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 <p>This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.</p>
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 <pre class="r"><code>ggtree(tree) + geom_tiplab() + xlim(0, 0.06)</code></pre>
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 <h2><i class="fa fa-angle-double-right"></i> Modify (tip) labels</h2>
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 <p>This could be easily done via the <code>%&lt;+%</code> operator to attach the modified version of the labels and than use <code>geom_tiplab</code> to display the modified version.</p>
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 <pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)
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 d = data.frame(label=lb, label2 = paste(&quot;AA&quot;, substring(lb, 1, 5)))
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 ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>
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 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
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 <h2><i class="fa fa-angle-double-right"></i> Formatting (tip) labels</h2>
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 <p>If you want to format labels, you need to set <code>parse=TRUE</code> in <code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be parsed into expression and displayed as described in <code>?plotmath</code>.</p>
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 <p>For example, the tiplabels contains two parts, species name and accession number and we want to display species name in <em>italic</em>, we can use command like this:</p>
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     geom_tiplab(aes(label=paste0(&#39;italic(&#39;, genus, &#39;)~bolditalic(&#39;, species, &#39;)~&#39;, geo)), parse=T)</code></pre>
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 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM" class="uri">https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM</a>.</p>
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 <h2><i class="fa fa-angle-double-right"></i> Avoid overlapping text labels</h2>
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 <p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a> package to repel overlapping text labels.</p>
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 <p>For example:</p>
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 raxml &lt;- read.raxml(raxml_file)
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 ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))</code></pre>
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 <p>For details, please refer to <a href="https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html">ggrepel usage examples</a>.</p>
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 <h2><i class="fa fa-angle-double-right"></i> bootstrap values from newick format</h2>
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 <p>It’s quite command to store <code>bootstrap</code> value as node label in <code>newick</code> format. Visualizing node label is easy using <code>geom_text2(aes(subset = !isTip, label=label))</code>.</p>
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 <p>If you want to only display a subset of <code>bootstrap</code> (e.g. bootstrap &gt; 80), you can’t simply using <code>geom_text2(subset= (label &gt; 80), label=label)</code> since <code>label</code> is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use <code>geom_text2(subset=(as.numeric(label) &gt; 80), label=label)</code>, it will also fail since <code>NAs</code> were introduced by coercion. We need to convert <code>NAs</code> to logical <code>FALSE</code>, this can be done by the following code:</p>
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 d &lt;- d[d$label &gt; 80,]
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 q + geom_text(data=d, aes(label=label))</code></pre>
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 <h1><i class="fa fa-map-marker"></i> <em>aesthetic</em> mapping</h1>
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 <h2><i class="fa fa-angle-double-right"></i> inherit <em>aes</em></h2>
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 <pre class="r"><code>ggtree(rtree(30)) + geom_point()</code></pre>
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 <p>For example, we can add symbolic points to nodes with <code>geom_point()</code> directly. The magic here is we don’t need to map <code>x</code> and <code>y</code> position of the points by providing <code>aes(x, y)</code> to <code>geom_point()</code> since it was already mapped by <code>ggtree</code> function and it serves as a global mapping for all layers.</p>
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 <p>But what if we provide a <code>dataset</code> in a layer and the <code>dataset</code> doesn’t contain column of <code>x</code> and/or <code>y</code>, the layer function also try to map <code>x</code> and <code>y</code> and also others if you map them in <code>ggtree</code> function. As these variable is not available in your <code>dataset</code>, you will get the following error:</p>
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 <pre><code>Error in eval(expr, envir, enclos) : object &#39;x&#39; not found</code></pre>
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 <p>This can be fixed by using parameter <code>inherit.aes=FALSE</code> which will disable inheriting mapping from <code>ggtree</code> function.</p>
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 <h2><i class="fa fa-angle-double-right"></i> use <code>$</code> in aes</h2>
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 <p>NEVER DO THIS.</p>
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 <p>see the explaination in the <a href="https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes">ggplot2 book 2ed</a>:</p>
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 <p>Never refer to a variable with <code>$</code> (e.g., <code>diamonds$carat</code>) in <code>aes()</code>. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.</p>
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 </blockquote>
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 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
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 <p>see my blog post: <a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a> and also my answer on <a href="https://github.com/GuangchuangYu/ggtree/issues/76" class="uri">https://github.com/GuangchuangYu/ggtree/issues/76</a> and <a href="https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8" class="uri">https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8</a>.</p>
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         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>
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 <p><a href="http://science.sciencemag.org/content/358/6364/789.full">Integrated view of <em>Vibrio cholerae</em> in the Americas</a>. *<strong>Science</strong>, 2017, 358(6364):789-793.</p>
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 <p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging</a>. <strong><em>PNAS</em></strong>, 2017, 114(5):1105-111-.</p>
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 <p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376617/">Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus</a>. <strong><em>Frontiers in Microbiology</em></strong>, 2017, 8:543</p>
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 <p><a href="http://aem.asm.org/content/82/22/6788.short">Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine</a>. <strong><em>Applied and Environmental Microbiology</em></strong>. 2016, 82(22):6788-6798.</p>
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         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>
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 <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>
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 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
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 <p>Please cite the following article when using <code>ggtree</code>:</p>
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 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-336-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-47-blue.svg?style=flat" alt="citation" /></a></p>
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 <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>
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 <h2><i class="fa fa-pencil"></i> Featured Articles</h2>
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+<p><img src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
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 <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>
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 <h2><i class="fa fa-download"></i> Installation</h2>
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 <p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor page</a>:</p>
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 ## biocLite(&quot;BiocUpgrade&quot;) ## you may need this
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 biocLite(&quot;ggtree&quot;)</code></pre>
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 <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>
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 <h4><i class="fa fa-angle-double-right"></i> Getting tree into R</h4>
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 <ul>
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 <li>tree parsers: bring evolution evidences to be used/analyzed in <code>R</code></li>
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 <li><code>merge_tree</code>: allows evolution evidences to be merged and compared</li>
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 <li><code>fortify</code> methods: convert tree objects into tidy data frame</li>
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 </ul>
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 <h4><i class="fa fa-angle-double-right"></i> Tree visualization &amp; annotation</h4>
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 <ul>
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 <li>parsing tree as a collection of nodes allows grammar of graphics to be supported</li>
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 <li>several layers and functions for tree annotation</li>
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 <li>supports annotating phylogenetic trees with user’s own data</li>
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 </ul>
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 <h4><i class="fa fa-angle-double-right"></i> Tree manipulation</h4>
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 <ul>
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 <li>helper functions for tree manipulation, make it possible to explore the tree visually</li>
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 </ul>
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 <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>
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 <h4><i class="fa fa-angle-double-right"></i> CRAN packages</h4>
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 <ul>
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 <li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle Phylogenetic Distance Matrices and Other Utilities</li>
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 </ul>
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 <h4><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
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 <ul>
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 <li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li>
423 414
 <li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>: Analyze high-throughput sequencing of T and B cell receptors</li>
424 415
 <li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>
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 </ul>
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 <h4><i class="fa fa-angle-double-right"></i> Other applications</h4>
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 <ul>
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 <li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li>
431 422
 <li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li>
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 <li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies created along a genome for patterns</li>
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 <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>
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       <pubDate>Thu, 06 Jul 2017 12:08:13 +0100</pubDate>
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-      <description>Plea to against BMC BMC journal protects paper of plagiarism https://t.co/FfSv7dPFXV @RetractionWatch @C0PE
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-&amp;mdash; Guangchuang Yu (@guangchuangyu) November 10, 2017     
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-The ggtree package extending the ggplot2 package. It based on grammar of graphics and takes all the good parts of ggplot2. ggtree is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. ggtree is released within the Bioconductor project and the source code is hosted on  GitHub.</description>
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+      <description>The ggtree package extending the ggplot2 package. It based on grammar of graphics and takes all the good parts of ggplot2. ggtree is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. ggtree is released within the Bioconductor project and the source code is hosted on  GitHub.
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+ Authors Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</description>
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       <description>http://dx.doi.org/10.1126/science.aao2136
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- https://doi.org/10.1186/s40168-017-0331-1
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- https://doi.org/10.1111/syen.12249
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- https://doi.org/10.1186/s12915-017-0402-6
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- https://doi.org/10.3389/fmicb.2017.00456
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+https://doi.org/10.1111/syen.12249
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 http://dx.doi.org/10.1111/2041-210X.12628
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- http://dx.doi.org/10.1016/j.meegid.2015.12.006</description>
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           <li>
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-            <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">
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-              Contact via email
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-            </a>
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+              <a href="mailto:guangchuangyu@gmail.com" title="Email of guangchuangyu@gmail.com">
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           </li>
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         </ul>
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+        <center><span class="zaln"><a href="https://guangchuangyu.github.io/2017/11/bmc-journal-protects-paper-of-plagiarism/" class="zb">Plea to against BMC</a></span></center>
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         <center><span class="zaln"><a href="https://mp.weixin.qq.com/s?__biz=MzI5NjUyNzkxMg==&mid=2247484170&idx=1&sn=ce5f7eb6df66d79661276a64bf25b4bc&chksm=ec43b24ddb343b5b2877574153aeccd049a6824716063883edb35c2338bd32c067caf3885f53#rd" class="zb">赞赏</a></span></center>
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <h2><i class="fa fa-book"></i> Vignettes</h2>
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 <ul>
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 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree utilities</a></li>
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 <li><a href="https://cran.r-project.org/web/packages/emojifont/vignettes/phylomoji.html">Phylomoji</a></li>
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 </ul>
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 <h2><i class="fa fa-wordpress"></i> Blog posts</h2>
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 <h3><i class="fa fa-angle-double-right"></i> News and updates</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>
36 36
 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>
42 42
 <li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>
43 43
 <li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
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 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
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 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
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 </ul>
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 <h3><i class="fa fa-angle-double-right"></i> Application</h3>
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 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
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 <li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>
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 <li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>
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 <h3><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
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 <li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>
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 <h2><i class="fa fa-slideshare"></i> Slides</h2>
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 <li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>
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 <li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>
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 <h2><i class="fa fa-youtube-play"></i> Video</h2>
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 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
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 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
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 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
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 <li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <h1><i class="fa fa-download"></i> Installation</h1>
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 <h2><i class="fa fa-angle-double-right"></i> Could not find function</h2>
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 <p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this error</a>, please make sure you are using the latest R and <code>ggtree</code>.</p>
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 <p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to <code>devel</code> branch.</p>
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 <p>Sometimes I may write blog post to introduce new functions which is not available in <code>release</code> branch, you need to install the <code>devel</code> version of <code>ggtree</code> in order to use these new functions.</p>
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 <p>You can download the <code>devel</code> version of <code>ggtree</code> from <a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html" class="uri">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and install it, or install the github version of <code>ggtree</code>.</p>
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 <p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>, <code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the <code>could not find function</code> error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.</p>
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+<section id="tip-label-truncated" class="level2">
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 <h2><i class="fa fa-angle-double-right"></i> Tip label truncated</h2>
25 25
 <p>ggplot2 can’t auto adjust xlim based on added text.</p>
26 26
 <pre class="r"><code>library(ggtree)
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@@ -29,8 +29,8 @@ tree&lt;-read.tree(text=&quot;(Organism1.006G249400.1:0.03977,(Organism2.022118m
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 ggtree(tree) + geom_tiplab()</code></pre>
30 30
 <p>This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.</p>
31 31
 <pre class="r"><code>ggtree(tree) + geom_tiplab() + xlim(0, 0.06)</code></pre>
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 <h2><i class="fa fa-angle-double-right"></i> Modify (tip) labels</h2>
35 35
 <p>This could be easily done via the <code>%&lt;+%</code> operator to attach the modified version of the labels and than use <code>geom_tiplab</code> to display the modified version.</p>
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 <pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)
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@@ -40,8 +40,8 @@ lb = get.tree(raxml)$tip.label
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 d = data.frame(label=lb, label2 = paste(&quot;AA&quot;, substring(lb, 1, 5)))
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 ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>
42 42
 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
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-<div id="formatting-tip-labels" class="section level2">
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+</section>
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+<section id="formatting-tip-labels" class="level2">
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 <h2><i class="fa fa-angle-double-right"></i> Formatting (tip) labels</h2>
46 46
 <p>If you want to format labels, you need to set <code>parse=TRUE</code> in <code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be parsed into expression and displayed as described in <code>?plotmath</code>.</p>
47 47
 <p>For example, the tiplabels contains two parts, species name and accession number and we want to display species name in <em>italic</em>, we can use command like this:</p>
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@@ -58,8 +58,8 @@ d &lt;- data.frame(label = tr$tip.label, genus = genus,
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 ggtree(tr) %&lt;+% d + xlim(NA, 5) +
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     geom_tiplab(aes(label=paste0(&#39;italic(&#39;, genus, &#39;)~bolditalic(&#39;, species, &#39;)~&#39;, geo)), parse=T)</code></pre>
60 60
 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM" class="uri">https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM</a>.</p>
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-<div id="avoid-overlapping-text-labels" class="section level2">
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 <h2><i class="fa fa-angle-double-right"></i> Avoid overlapping text labels</h2>
64 64
 <p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a> package to repel overlapping text labels.</p>
65 65
 <p>For example:</p>
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@@ -69,8 +69,8 @@ raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitions
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 raxml &lt;- read.raxml(raxml_file)
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 ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))</code></pre>
71 71
 <p>For details, please refer to <a href="https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html">ggrepel usage examples</a>.</p>
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 <h2><i class="fa fa-angle-double-right"></i> bootstrap values from newick format</h2>
75 75
 <p>It’s quite command to store <code>bootstrap</code> value as node label in <code>newick</code> format. Visualizing node label is easy using <code>geom_text2(aes(subset = !isTip, label=label))</code>.</p>
76 76
 <p>If you want to only display a subset of <code>bootstrap</code> (e.g. bootstrap &gt; 80), you can’t simply using <code>geom_text2(subset= (label &gt; 80), label=label)</code> since <code>label</code> is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use <code>geom_text2(subset=(as.numeric(label) &gt; 80), label=label)</code>, it will also fail since <code>NAs</code> were introduced by coercion. We need to convert <code>NAs</code> to logical <code>FALSE</code>, this can be done by the following code:</p>
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@@ -85,19 +85,19 @@ d$label &lt;- as.numeric(d$label)
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 d &lt;- d[d$label &gt; 80,]
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 q + geom_text(data=d, aes(label=label))</code></pre>
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 <h1><i class="fa fa-map-marker"></i> <em>aesthetic</em> mapping</h1>
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 <h2><i class="fa fa-angle-double-right"></i> inherit <em>aes</em></h2>
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 <pre class="r"><code>ggtree(rtree(30)) + geom_point()</code></pre>
95 95
 <p>For example, we can add symbolic points to nodes with <code>geom_point()</code> directly. The magic here is we don’t need to map <code>x</code> and <code>y</code> position of the points by providing <code>aes(x, y)</code> to <code>geom_point()</code> since it was already mapped by <code>ggtree</code> function and it serves as a global mapping for all layers.</p>
96 96
 <p>But what if we provide a <code>dataset</code> in a layer and the <code>dataset</code> doesn’t contain column of <code>x</code> and/or <code>y</code>, the layer function also try to map <code>x</code> and <code>y</code> and also others if you map them in <code>ggtree</code> function. As these variable is not available in your <code>dataset</code>, you will get the following error:</p>
97 97
 <pre><code>Error in eval(expr, envir, enclos) : object &#39;x&#39; not found</code></pre>
98 98
 <p>This can be fixed by using parameter <code>inherit.aes=FALSE</code> which will disable inheriting mapping from <code>ggtree</code> function.</p>
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 <h2><i class="fa fa-angle-double-right"></i> use <code>$</code> in aes</h2>
102 102
 <p>NEVER DO THIS.</p>
103 103
 <p>see the explaination in the <a href="https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes">ggplot2 book 2ed</a>:</p>
... ...
@@ -105,12 +105,12 @@ q + geom_text(data=d, aes(label=label))</code></pre>
105 105
 <p>Never refer to a variable with <code>$</code> (e.g., <code>diamonds$carat</code>) in <code>aes()</code>. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.</p>
106 106
 </blockquote>
107 107
 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
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 <h1><i class="fa fa-tree"></i> Annotation</h1>
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 <h2><i class="fa fa-angle-double-right"></i> colouring edges by user data</h2>
114 114
 <p>see my blog post: <a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a> and also my answer on <a href="https://github.com/GuangchuangYu/ggtree/issues/76" class="uri">https://github.com/GuangchuangYu/ggtree/issues/76</a> and <a href="https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8" class="uri">https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8</a>.</p>
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
10 10
 <p><a href="https://github.com/GuangchuangYu/featured_img">Let us know</a> if you have published using <code>ggtree</code> and your publication will be featured here.</p>
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 <p><img src="../images/citation.png" width="880"/></p>
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 <h2><i class="fa fa-calendar"></i> 2017</h2>
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 <p><a href="http://science.sciencemag.org/content/358/6364/789.full">Integrated view of <em>Vibrio cholerae</em> in the Americas</a>. *<strong>Science</strong>, 2017, 358(6364):789-793.</p>
15 15
 <p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging</a>. <strong><em>PNAS</em></strong>, 2017, 114(5):1105-111-.</p>
16 16
 <p><a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376617/">Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus</a>. <strong><em>Frontiers in Microbiology</em></strong>, 2017, 8:543</p>
17 17
 <p><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3">Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in <em>Bacteroides coprocola</em></a>. <strong><em>Microbiome</em></strong>, 2017, 5:15</p>
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 <h2><i class="fa fa-calendar"></i> 2016</h2>
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 <p><a href="http://aem.asm.org/content/82/22/6788.short">Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine</a>. <strong><em>Applied and Environmental Microbiology</em></strong>. 2016, 82(22):6788-6798.</p>
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-{{% tweet "928836702998638592" %}}
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 <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>
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 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
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-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21118/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
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+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.1-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21262/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
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 <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>
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 <h2><i class="fa fa-user"></i> Authors</h2>
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 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
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 <h2><i class="fa fa-book"></i> Citation</h2>
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 <p>Please cite the following article when using <code>ggtree</code>:</p>
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 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-336-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-47-blue.svg?style=flat" alt="citation" /></a></p>
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 <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>
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 <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>
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 <h2><i class="fa fa-download"></i> Installation</h2>
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 <p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor page</a>:</p>
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 <pre class="r"><code>## try http:// if https:// URLs are not supported
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@@ -42,18 +34,18 @@ source(&quot;https://bioconductor.org/biocLite.R&quot;)
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 ## biocLite(&quot;BiocUpgrade&quot;) ## you may need this
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 biocLite(&quot;ggtree&quot;)</code></pre>
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 <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>
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-</div>
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-<div id="overview" class="section level2">
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+</section>
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+<section id="overview" class="level2">
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 <h2><i class="fa fa-cogs"></i> Overview</h2>
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-<div id="getting-tree-into-r" class="section level4">
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+<section id="getting-tree-into-r" class="level4">
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 <h4><i class="fa fa-angle-double-right"></i> Getting tree into R</h4>
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 <ul>
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 <li>tree parsers: bring evolution evidences to be used/analyzed in <code>R</code></li>
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 <li><code>merge_tree</code>: allows evolution evidences to be merged and compared</li>
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 <li><code>fortify</code> methods: convert tree objects into tidy data frame</li>
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 </ul>
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-</div>
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-<div id="tree-visualization-annotation" class="section level4">
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+</section>
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+<section id="tree-visualization-annotation" class="level4">
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 <h4><i class="fa fa-angle-double-right"></i> Tree visualization &amp; annotation</h4>
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 <ul>
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 <li>parsing tree as a collection of nodes allows grammar of graphics to be supported</li>
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@@ -61,41 +53,41 @@ biocLite(&quot;ggtree&quot;)</code></pre>
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 <li>several layers and functions for tree annotation</li>
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 <li>supports annotating phylogenetic trees with user’s own data</li>
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 </ul>
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-</div>
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-<div id="tree-manipulation" class="section level4">
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+</section>
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+<section id="tree-manipulation" class="level4">
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 <h4><i class="fa fa-angle-double-right"></i> Tree manipulation</h4>
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 <ul>
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 <li>helper functions for tree manipulation, make it possible to explore the tree visually</li>
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 </ul>
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 <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>
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-</div>
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-</div>
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-<div id="projects-that-depend-on-ggtree" class="section level2">
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+</section>
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+</section>
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+<section id="projects-that-depend-on-ggtree" class="level2">
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 <h2><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>
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-<div id="cran-packages" class="section level4">
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+<section id="cran-packages" class="level4">
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 <h4><i class="fa fa-angle-double-right"></i> CRAN packages</h4>
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 <ul>
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 <li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle Phylogenetic Distance Matrices and Other Utilities</li>
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 </ul>
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-</div>
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-<div id="bioconductor-packages" class="section level4">
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+</section>
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+<section id="bioconductor-packages" class="level4">
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 <h4><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
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 <ul>
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 <li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li>
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 <li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>: Analyze high-throughput sequencing of T and B cell receptors</li>
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 <li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>
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 </ul>
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-</div>
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-<div id="other-applications" class="section level4">
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+</section>
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+<section id="other-applications" class="level4">
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 <h4><i class="fa fa-angle-double-right"></i> Other applications</h4>
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 <ul>
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 <li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li>
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 <li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li>
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 <li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies created along a genome for patterns</li>
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 </ul>
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-</div>
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-</div>
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-<div id="feedback" class="section level2">
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+</section>
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+</section>
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+<section id="feedback" class="level2">
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 <h2><i class="fa fa-comments"></i> Feedback</h2>
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 <ul class="fa-ul">
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 <li>
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@@ -114,4 +106,4 @@ biocLite(&quot;ggtree&quot;)</code></pre>
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 <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>
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 </li>
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 </ul>
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-</div>
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+</section>
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@@ -7,15 +7,6 @@ weight: 1
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-## Plea to against BMC
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-
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-```{r echo=FALSE}
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-blogdown::shortcode('tweet', '928836702998638592')
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-```
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-
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-
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-
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css">
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