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update docs

guangchuang yu authored on 04/12/2017 05:47:36
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@@ -7,14 +7,14 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)
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 [![develVersion](https://img.shields.io/badge/devel%20version-1.11.1-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
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-[![total](https://img.shields.io/badge/downloads-21527/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 state and is being actively
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 developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)
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 [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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-[![Last-changedate](https://img.shields.io/badge/last%20change-2017--11--24-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)
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@@ -59,8 +59,8 @@ their covariates and other associated data. ***Methods in Ecology and
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 Evolution***. 2017, 8(1):28-36.
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 [![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
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-[![citation](https://img.shields.io/badge/cited%20by-49-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![Altmetric](https://img.shields.io/badge/Altmetric-333-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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+[![citation](https://img.shields.io/badge/cited%20by-51-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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@@ -71,7 +71,7 @@ Evolution***. 2017, 8(1):28-36.
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 ### Download stats
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 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![total](https://img.shields.io/badge/downloads-21527/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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@@ -344,7 +344,7 @@
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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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-<section id="vignettes" class="level2">
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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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@@ -356,10 +356,10 @@
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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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-</section>
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-<section id="blog-posts" class="level2">
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+</div>
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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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-<section id="news-and-updates" class="level3">
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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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@@ -371,16 +371,16 @@
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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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-</section>
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-<section id="data-manipulation" class="level3">
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+</div>
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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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-</section>
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-<section id="tree-visualization" class="level3">
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+</div>
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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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@@ -389,8 +389,8 @@
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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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-</section>
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-<section id="tree-annotation" class="level3">
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+</div>
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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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@@ -406,14 +406,14 @@
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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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-</section>
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-<section id="tree-manipulation" class="level3">
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+</div>
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+<div id="tree-manipulation" class="section level3">
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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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-</section>
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-<section id="application" class="level3">
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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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-</section>
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-<section id="funny-stuff" class="level3">
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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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-</section>
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-<section id="slides" class="level2">
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+</div>
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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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-</section>
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-<section id="video" class="level2">
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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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-</section>
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-<section id="workflow" class="level2">
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 <h2><i class="fa fa-gift"></i> Workflow</h2>
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 <ul>
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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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 </ul>
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 			<aside class="copyright" role="note">
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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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-<section id="installation" class="level1">
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 <h1><i class="fa fa-download"></i> Installation</h1>
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-<section id="could-not-find-function" class="level2">
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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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@@ -366,8 +366,8 @@ tree&lt;-read.tree(text=&quot;(Organism1.006G249400.1:0.03977,(Organism2.022118m
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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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-</section>
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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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 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>
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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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@@ -442,15 +442,15 @@ q + geom_text(data=d, aes(label=label))</code></pre>
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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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 <h1><i class="fa fa-tree"></i> Annotation</h1>
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-<section id="colouring-edges-by-user-data" class="level2">
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 <h2><i class="fa fa-angle-double-right"></i> colouring edges by user data</h2>
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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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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <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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 <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>
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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="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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 				<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-1.11.1-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><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-21911/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><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-333-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-51-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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 <pre class="r"><code>## try http:// if https:// URLs are not supported
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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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 <h2><i class="fa fa-cogs"></i> Overview</h2>
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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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 <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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 <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>
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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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 <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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 <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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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">The R <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> is now published in <a href="https://twitter.com/MethodsEcolEvol?ref_src=twsrc%5Etfw">@MethodsEcolEvol</a> <a href="https://t.co/6fvSRQo2CC">https://t.co/6fvSRQo2CC</a> <a href="https://twitter.com/hashtag/evomics2017?src=hash&amp;ref_src=twsrc%5Etfw">#evomics2017</a> <a href="https://t.co/Dwq1DD84A2">pic.twitter.com/Dwq1DD84A2</a></p>&mdash; Elin Videvall (@ElinVidevall) <a href="https://twitter.com/ElinVidevall/status/822383911258890242?ref_src=twsrc%5Etfw">January 20, 2017</a></blockquote>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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-<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Assortative tip coloring by text string using <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> by <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> <a href="https://t.co/rocvFK3OOS">https://t.co/rocvFK3OOS</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/mEMkhZ2fVk">pic.twitter.com/mEMkhZ2fVk</a></p>&mdash; Guanyang Zhang (@GYZhang2) <a href="https://twitter.com/GYZhang2/status/811666431452450816?ref_src=twsrc%5Etfw">December 21, 2016</a></blockquote>
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+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Assortative tip coloring by text string using <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> by <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> <a href="https://t.co/rocvFK3OOS">https://t.co/rocvFK3OOS</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/mEMkhZ2fVk">pic.twitter.com/mEMkhZ2fVk</a></p>&mdash; Guanyang Zhang 张冠阳 (@GYZhang2) <a href="https://twitter.com/GYZhang2/status/811666431452450816?ref_src=twsrc%5Etfw">December 21, 2016</a></blockquote>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">Featured this week: ggtree, an R package for visualization &amp; annotation of phylogenetic trees. Like it? Vote it up! <a href="https://t.co/laxtuRQDGB">https://t.co/laxtuRQDGB</a> <a href="https://t.co/zDvEBysWSQ">pic.twitter.com/zDvEBysWSQ</a></p>&mdash; LabWorm (@TheLabWorm) <a href="https://twitter.com/TheLabWorm/status/811661275889549312?ref_src=twsrc%5Etfw">December 21, 2016</a></blockquote>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">am quite liking <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://twitter.com/hashtag/ggplot?src=hash&amp;ref_src=twsrc%5Etfw">#ggplot</a> <a href="https://t.co/hvywS2z4ps">pic.twitter.com/hvywS2z4ps</a></p>&mdash; Nicholas E Ilott (@IlottNick) <a href="https://twitter.com/IlottNick/status/788751417746059264?ref_src=twsrc%5Etfw">October 19, 2016</a></blockquote>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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-<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Treespace visualization of a heuristic best tree search in <a href="https://twitter.com/hashtag/R?src=hash&amp;ref_src=twsrc%5Etfw">#R</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/hnSJpIABql">pic.twitter.com/hnSJpIABql</a></p>&mdash; Alejandro Damián Serrano ⑂🌊🔬 (@antropoteuthis) <a href="https://twitter.com/antropoteuthis/status/693123105707986944?ref_src=twsrc%5Etfw">January 29, 2016</a></blockquote>
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+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Treespace visualization of a heuristic best tree search in <a href="https://twitter.com/hashtag/R?src=hash&amp;ref_src=twsrc%5Etfw">#R</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/hnSJpIABql">pic.twitter.com/hnSJpIABql</a></p>&mdash; 𝓐𝖑𝖊𝖏𝖆𝖓𝖉𝖗𝖔 𝕯𝖆𝖒𝖎𝖆𝖓 𝓢𝖊𝖗𝖗𝖆𝖓𝖔 ⑂ (@antropoteuthis) <a href="https://twitter.com/antropoteuthis/status/693123105707986944?ref_src=twsrc%5Etfw">January 29, 2016</a></blockquote>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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 <blockquote class="twitter-tweet"><p lang="en" dir="ltr"><a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> Updated to latest <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> and <a href="https://twitter.com/hashtag/ggplot2?src=hash&amp;ref_src=twsrc%5Etfw">#ggplot2</a> and very impressed! Any ideas on using geom_label with tip labels to add box/fill?</p>&mdash; Jo Williams-Newkirk (@ajwnewkirk) <a href="https://twitter.com/ajwnewkirk/status/691762302492790788?ref_src=twsrc%5Etfw">January 25, 2016</a></blockquote>
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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>
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 <h3><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
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 <ul>
41 41
 <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>
44 44
 </ul>
45
-</section>
46
-<section id="tree-visualization" class="level3">
45
+</div>
46
+<div id="tree-visualization" class="section level3">
47 47
 <h3><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
48 48
 <ul>
49 49
 <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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@@ -52,8 +52,8 @@ weight: 10
52 52
 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
53 53
 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
54 54
 </ul>
55
-</section>
56
-<section id="tree-annotation" class="level3">
55
+</div>
56
+<div id="tree-annotation" class="section level3">
57 57
 <h3><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
58 58
 <ul>
59 59
 <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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@@ -69,14 +69,14 @@ weight: 10
69 69
 <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>
70 70
 <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>
71 71
 </ul>
72
-</section>
73
-<section id="tree-manipulation" class="level3">
72
+</div>
73
+<div id="tree-manipulation" class="section level3">
74 74
 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
75 75
 <ul>
76 76
 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
77 77
 </ul>
78
-</section>
79
-<section id="application" class="level3">
78
+</div>
79
+<div id="application" class="section level3">
80 80
 <h3><i class="fa fa-angle-double-right"></i> Application</h3>
81 81
 <ul>
82 82
 <li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
... ...
@@ -84,34 +84,34 @@ weight: 10
84 84
 <li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>
85 85
 <li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>
86 86
 </ul>
87
-</section>
88
-<section id="funny-stuff" class="level3">
87
+</div>
88
+<div id="funny-stuff" class="section level3">
89 89
 <h3><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
90 90
 <ul>
91 91
 <li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>
92 92
 <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>
93 93
 <li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>
94 94
 </ul>
95
-</section>
96
-</section>
97
-<section id="slides" class="level2">
95
+</div>
96
+</div>
97
+<div id="slides" class="section level2">
98 98
 <h2><i class="fa fa-slideshare"></i> Slides</h2>
99 99
 <ul>
100 100
 <li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>
101 101
 <li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>
102 102
 </ul>
103
-</section>
104
-<section id="video" class="level2">
103
+</div>
104
+<div id="video" class="section level2">
105 105
 <h2><i class="fa fa-youtube-play"></i> Video</h2>
106 106
 <ul>
107 107
 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
108 108
 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
109 109
 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
110 110
 </ul>
111
-</section>
112
-<section id="workflow" class="level2">
111
+</div>
112
+<div id="workflow" class="section level2">
113 113
 <h2><i class="fa fa-gift"></i> Workflow</h2>
114 114
 <ul>
115 115
 <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>
116 116
 </ul>
117
-</section>
117
+</div>
... ...
@@ -7,20 +7,20 @@ weight: 20
7 7
 
8 8
 
9 9
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
10
-<section id="installation" class="level1">
10
+<div id="installation" class="section level1">
11 11
 <h1><i class="fa fa-download"></i> Installation</h1>
12
-<section id="could-not-find-function" class="level2">
12
+<div id="could-not-find-function" class="section level2">
13 13
 <h2><i class="fa fa-angle-double-right"></i> Could not find function</h2>
14 14
 <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>
15 15
 <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>
16 16
 <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>
17 17
 <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>
18 18
 <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>
19
-</section>
20
-</section>
21
-<section id="text-label" class="level1">
19
+</div>
20
+</div>
21
+<div id="text-label" class="section level1">
22 22
 <h1><i class="fa fa-text-height"></i> Text &amp; Label</h1>
23
-<section id="tip-label-truncated" class="level2">
23
+<div id="tip-label-truncated" class="section level2">
24 24
 <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)
... ...
@@ -29,8 +29,8 @@ tree&lt;-read.tree(text=&quot;(Organism1.006G249400.1:0.03977,(Organism2.022118m
29 29
 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>
32
-</section>
33
-<section id="modify-tip-labels" class="level2">
32
+</div>
33
+<div id="modify-tip-labels" class="section level2">
34 34
 <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>
36 36
 <pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)
... ...
@@ -40,8 +40,8 @@ lb = get.tree(raxml)$tip.label
40 40
 d = data.frame(label=lb, label2 = paste(&quot;AA&quot;, substring(lb, 1, 5)))
41 41
 ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>
42 42
 <p>see also <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a> and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
43
-</section>
44
-<section id="formatting-tip-labels" class="level2">
43
+</div>
44
+<div id="formatting-tip-labels" class="section level2">
45 45
 <h2><i class="fa fa-angle-double-right"></i> Formatting (tip) labels</h2>
46 46
 <p>If you want to format labels, you need to set <code>parse=TRUE</code> in <code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be parsed into expression and displayed as described in <code>?plotmath</code>.</p>
47 47
 <p>For example, the tiplabels contains two parts, species name and accession number and we want to display species name in <em>italic</em>, we can use command like this:</p>
... ...
@@ -58,8 +58,8 @@ d &lt;- data.frame(label = tr$tip.label, genus = genus,
58 58
 ggtree(tr) %&lt;+% d + xlim(NA, 5) +
59 59
     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>
61
-</section>
62
-<section id="avoid-overlapping-text-labels" class="level2">
61
+</div>
62
+<div id="avoid-overlapping-text-labels" class="section level2">
63 63
 <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>
... ...
@@ -69,8 +69,8 @@ raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitions
69 69
 raxml &lt;- read.raxml(raxml_file)
70 70
 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>
72
-</section>
73
-<section id="bootstrap-values-from-newick-format" class="level2">
72
+</div>
73
+<div id="bootstrap-values-from-newick-format" class="section level2">
74 74
 <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>
... ...
@@ -85,19 +85,19 @@ d$label &lt;- as.numeric(d$label)
85 85
 d &lt;- d[d$label &gt; 80,]
86 86
 
87 87
 q + geom_text(data=d, aes(label=label))</code></pre>
88
-</section>
89
-</section>
90
-<section id="aesthetic-mapping" class="level1">
88
+</div>
89
+</div>
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+<div id="aesthetic-mapping" class="section level1">
91 91
 <h1><i class="fa fa-map-marker"></i> <em>aesthetic</em> mapping</h1>
92
-<section id="inherit-aes" class="level2">
92
+<div id="inherit-aes" class="section level2">
93 93
 <h2><i class="fa fa-angle-double-right"></i> inherit <em>aes</em></h2>
94 94
 <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>
99
-</section>
100
-<section id="use-in-aes" class="level2">
99
+</div>
100
+<div id="use-in-aes" class="section level2">
101 101
 <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>
108
-</section>
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-</section>
110
-<section id="annotation" class="level1">
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+</div>
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+</div>
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+<div id="annotation" class="section level1">
111 111
 <h1><i class="fa fa-tree"></i> Annotation</h1>
112
-<section id="colouring-edges-by-user-data" class="level2">
112
+<div id="colouring-edges-by-user-data" class="section level2">
113 113
 <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>
115
-</section>
116
-</section>
115
+</div>
116
+</div>
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@@ -9,14 +9,14 @@ weight: 30
9 9
 <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>
11 11
 <p><img src="../images/citation.png" width="880"/></p>
12
-<section id="section" class="level2">
12
+<div id="section" class="section level2">
13 13
 <h2><i class="fa fa-calendar"></i> 2017</h2>
14 14
 <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>
18
-</section>
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+</div>
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+<div id="section-1" class="section level2">
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 <h2><i class="fa fa-calendar"></i> 2016</h2>
21 21
 <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>
22
-</section>
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+</div>
... ...
@@ -9,24 +9,24 @@ weight: 1
9 9
 
10 10
 <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>
11 11
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
12
-<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>
12
+<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-21911/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>
13 13
 <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>
14
-<section id="authors" class="level2">
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+<div id="authors" class="section level2">
15 15
 <h2><i class="fa fa-user"></i> Authors</h2>
16 16
 <p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
17
-</section>
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-<section id="citation" class="level2">
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+</div>
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+<div id="citation" class="section level2">
19 19
 <h2><i class="fa fa-book"></i> Citation</h2>
20 20
 <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><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-333-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-51-blue.svg?style=flat" alt="citation" /></a></p>
22 22
 <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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+</div>
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+<div id="featured-articles" class="section level2">
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 <h2><i class="fa fa-pencil"></i> Featured Articles</h2>
26 26
 <p><img src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
27 27
 <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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+</div>
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+<div id="installation" class="section level2">
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 <h2><i class="fa fa-download"></i> Installation</h2>
31 31
 <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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@@ -34,18 +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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-<section id="overview" class="level2">
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 <h2><i class="fa fa-cogs"></i> Overview</h2>
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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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-</section>
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-<section id="tree-visualization-annotation" class="level4">
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+</div>
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+<div id="tree-visualization-annotation" class="section 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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 <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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-<section id="projects-that-depend-on-ggtree" class="level2">
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+</div>
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 <h2><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>
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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 id="bioconductor-packages" class="section 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>
77 77
 <li><a href="https://www.bioconductor.org/packages/LymphoSeq">LymphoSeq</a>: Analyze high-throughput sequencing of T and B cell receptors</li>
78 78
 <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>
85 85
 <li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li>
86 86
 <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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-<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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 <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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