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update docs

guangchuang yu authored on 08/11/2017 13:11:39
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@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues
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 Packaged: 2014-12-03 08:16:14 UTC; root
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 biocViews: Alignment, Annotation, Clustering, DataImport,
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     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
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-RoxygenNote: 6.0.1
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+RoxygenNote: 6.0.1.9000
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@@ -190,6 +190,8 @@ importFrom(magrittr,add)
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 importFrom(magrittr,equals)
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 importFrom(methods,is)
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 importFrom(methods,missingArg)
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+importFrom(methods,setGeneric)
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+importFrom(methods,setOldClass)
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 importFrom(rvcheck,get_fun_from_pkg)
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 importFrom(scales,alpha)
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 importFrom(tidyr,gather)
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@@ -1,5 +1,6 @@
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 ## setOldClass("phylo")
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 ## setOldClass("multiPhylo")
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+##' @importFrom methods setOldClass
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 setOldClass("ggtree")
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@@ -30,6 +30,7 @@ as.binary <- function(tree, ...) {
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 ##' @param node internal nnode number
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 ##' @param ... additional parameter
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 ##' @return tree object
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+##' @importFrom methods setGeneric
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 ##' @export
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 setGeneric("reroot", function(object, node, ...) standardGeneric("reroot"))
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@@ -79,10 +79,10 @@ GeomHilight <- ggproto("GeomHilight", Geom,
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                          # # Get layout
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                          #
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-                         # layout <- data[1,]$layout
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-                         #
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-                         # If layout is {"rectangular”, “slanted”, “fan”, “circular”, “radial”} then find set of points that define
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-                         # the retangular region around the clade.
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+                           ## layout <- data[1,]$layout
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+                           ##
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+                           ## If layout is ("rectangular”, "slanted", "fan", "circular", "radial") then find set of points that define
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+                           ## the retangular region around the clade.
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                          # if( layout %in% c('rectangular', 'slanted', 'fan', 'circular', 'radial') ){
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                          #
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                          #   # get number of clade nodes.
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.0-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-20560/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-986/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.0-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-20978/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--11--01-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--11--08-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
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@@ -27,7 +27,7 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, 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. ***Methods in Ecology and 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) [![Altmetric](https://img.shields.io/badge/Altmetric-338-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-42-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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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) [![Altmetric](https://img.shields.io/badge/Altmetric-337-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-45-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 ------------------------------------------------------------------------
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@@ -37,7 +37,7 @@ Please cite the following article when using `ggtree`:
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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) [![total](https://img.shields.io/badge/downloads-20560/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-986/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-20978/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 <img src="docs/images/dlstats.png" width="890"/>
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@@ -383,7 +383,16 @@ ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>
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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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 <pre><code>ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label=&#39;paste(italic(&quot;species name&quot;), &quot;accession number&quot;)&#39;, parse=T)</code></pre>
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 <p>Another example for formating all tip labels:</p>
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-<pre><code>ggtree(rtree(30)) + geom_tiplab(aes(label=paste0(&#39;bold(&#39;, label, &#39;)~italic(&#39;, node, &#39;)&#39;)), parse=TRUE)</code></pre>
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+<pre class="r"><code>ggtree(rtree(30)) + geom_tiplab(aes(label=paste0(&#39;bold(&#39;, label, &#39;)~italic(&#39;, node, &#39;)&#39;)), parse=TRUE)</code></pre>
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+<p>The <code>label</code> can be provided by a <code>data.frame</code> that contains related information of the taxa.</p>
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+<pre class="r"><code>tr &lt;- read.tree(text = &quot;((a,(b,c)),d);&quot;)
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+genus &lt;- c(&quot;Gorilla&quot;, &quot;Pan&quot;, &quot;Homo&quot;, &quot;Pongo&quot;)
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+species &lt;- c(&quot;gorilla&quot;, &quot;spp.&quot;, &quot;sapiens&quot;, &quot;pygmaeus&quot;)
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+geo &lt;- c(&quot;Africa&quot;, &quot;Africa&quot;, &quot;World&quot;, &quot;Asia&quot;)
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+d &lt;- data.frame(label = tr$tip.label, genus = genus,
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+                species = species, geo = geo)
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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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 </div>
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 <div id="avoid-overlapping-text-labels" class="section level2">
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Binary files a/docs/images/citation.png and b/docs/images/citation.png differ
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Binary files a/docs/images/dlstats.png and b/docs/images/dlstats.png differ
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@@ -345,7 +345,7 @@
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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-1.9.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-20560/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-986/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-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-20978/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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 <div id="authors" class="section level2">
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 <h2><i class="fa fa-user"></i> Authors</h2>
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@@ -354,7 +354,7 @@
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 <div id="citation" class="section level2">
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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-338-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-42-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-337-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-45-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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 </div>
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 <div id="featured-articles" class="section level2">
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@@ -47,7 +47,16 @@ ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))</code></pre>
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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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 <pre><code>ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label=&#39;paste(italic(&quot;species name&quot;), &quot;accession number&quot;)&#39;, parse=T)</code></pre>
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 <p>Another example for formating all tip labels:</p>
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-<pre><code>ggtree(rtree(30)) + geom_tiplab(aes(label=paste0(&#39;bold(&#39;, label, &#39;)~italic(&#39;, node, &#39;)&#39;)), parse=TRUE)</code></pre>
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+<pre class="r"><code>ggtree(rtree(30)) + geom_tiplab(aes(label=paste0(&#39;bold(&#39;, label, &#39;)~italic(&#39;, node, &#39;)&#39;)), parse=TRUE)</code></pre>
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+<p>The <code>label</code> can be provided by a <code>data.frame</code> that contains related information of the taxa.</p>
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+<pre class="r"><code>tr &lt;- read.tree(text = &quot;((a,(b,c)),d);&quot;)
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+genus &lt;- c(&quot;Gorilla&quot;, &quot;Pan&quot;, &quot;Homo&quot;, &quot;Pongo&quot;)
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+species &lt;- c(&quot;gorilla&quot;, &quot;spp.&quot;, &quot;sapiens&quot;, &quot;pygmaeus&quot;)
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+geo &lt;- c(&quot;Africa&quot;, &quot;Africa&quot;, &quot;World&quot;, &quot;Asia&quot;)
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+d &lt;- data.frame(label = tr$tip.label, genus = genus,
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+                species = species, geo = geo)
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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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 </div>
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 <div id="avoid-overlapping-text-labels" class="section level2">
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@@ -75,13 +75,26 @@ ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("speci
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 Another example for formating all tip labels:
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-```
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+```r
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 ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)
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 ```
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-see
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-also
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-<https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM>.
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+The `label` can be provided by a `data.frame` that contains related information
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+of the taxa.
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+
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+```r
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+tr <- read.tree(text = "((a,(b,c)),d);")
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+genus <- c("Gorilla", "Pan", "Homo", "Pongo")
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+species <- c("gorilla", "spp.", "sapiens", "pygmaeus")
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+geo <- c("Africa", "Africa", "World", "Asia")
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+d <- data.frame(label = tr$tip.label, genus = genus,
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+                species = species, geo = geo)
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+ggtree(tr) %<+% d + xlim(NA, 5) +
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+    geom_tiplab(aes(label=paste0('italic(', genus, ')~bolditalic(', species, ')~', geo)), parse=T)
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+```
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+
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+see also <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM>.
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+
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 ## <i class="fa fa-angle-double-right"></i> Avoid overlapping text labels
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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-1.9.4-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-20560/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-986/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-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-20978/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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 <div id="authors" class="section level2">
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 <h2><i class="fa fa-user"></i> Authors</h2>
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@@ -18,7 +18,7 @@ weight: 1
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 <div id="citation" class="section level2">
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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-338-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-42-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-337-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-45-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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 </div>
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
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