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guangchuang yu committed Aug 7, 2017
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -4,7 +4,7 @@ PKGSRC := $(shell basename `pwd`)

all: rd readme check clean

alldocs: rd readme mkdocs
alldocs: site rd readme

rd:
Rscript -e 'roxygen2::roxygenise(".")'
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8 changes: 4 additions & 4 deletions README.md
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Expand Up @@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

[![](https://img.shields.io/badge/release%20version-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.3-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) [![](https://img.shields.io/badge/download-17269/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
[![](https://img.shields.io/badge/release%20version-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.3-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) [![](https://img.shields.io/badge/download-17742/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-834/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

[![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--08--03-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)
[![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--08--07-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)

[![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)

Expand All @@ -27,7 +27,7 @@ Please cite the following article when using `ggtree`:

**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.

[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-29-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-347-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-30-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

------------------------------------------------------------------------

Expand All @@ -37,7 +37,7 @@ Please cite the following article when using `ggtree`:

### Download stats

[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-17269/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-17742/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-834/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

<img src="docs/images/dlstats.png" width="890"/>

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6 changes: 6 additions & 0 deletions docs/gallery/index.html
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Expand Up @@ -343,6 +343,12 @@ <h1>Gallery </h1>

<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
<div class="figure">
<img src="http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12915-017-0402-6/MediaObjects/12915_2017_402_Fig2_HTML.gif" />

</div>
<p><a href="https://doi.org/10.1186/s12915-017-0402-6" class="uri">https://doi.org/10.1186/s12915-017-0402-6</a></p>
<hr />
<div class="figure">
<img src="https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg" />

</div>
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7 changes: 7 additions & 0 deletions docs/gallery/index.rmd
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<link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">


![](http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12915-017-0402-6/MediaObjects/12915_2017_402_Fig2_HTML.gif)

<https://doi.org/10.1186/s12915-017-0402-6>

----


![](https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg)

<http://dx.doi.org/10.3389/fmicb.2017.00543>
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3 changes: 2 additions & 1 deletion docs/gallery/index.xml
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Expand Up @@ -18,7 +18,8 @@
<pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>

<guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
<description>http://dx.doi.org/10.3389/fmicb.2017.00543
<description>https://doi.org/10.1186/s12915-017-0402-6
http://dx.doi.org/10.3389/fmicb.2017.00543
https://doi.org/10.3389/fmicb.2017.00456
http://dx.doi.org/10.1186/s40168-017-0232-3
http://dx.doi.org/10.1111/2041-210X.12628
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4 changes: 2 additions & 2 deletions docs/index.html
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Expand Up @@ -344,7 +344,7 @@ <h1>ggtree: visualization and annotation of phylogenetic trees </h1>

<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>
<p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17269/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17742/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-834/month-blue.svg?style=flat" /></a></p>
<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>
<div id="authors" class="section level2">
<h2><i class="fa fa-user"></i> Authors</h2>
Expand All @@ -353,7 +353,7 @@ <h2><i class="fa fa-user"></i> Authors</h2>
<div id="citation" class="section level2">
<h2><i class="fa fa-book"></i> Citation</h2>
<p>Please cite the following article when using <code>ggtree</code>:</p>
<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" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat" /></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-29-blue.svg?style=flat" alt="citation" /></a></p>
<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" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-347-blue.svg?style=flat" /></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-30-blue.svg?style=flat" alt="citation" /></a></p>
<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>
</div>
<div id="featured-articles" class="section level2">
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Expand Up @@ -60,7 +60,8 @@ Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotid
<pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>

<guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
<description>http://dx.doi.org/10.3389/fmicb.2017.00543
<description>https://doi.org/10.1186/s12915-017-0402-6
http://dx.doi.org/10.3389/fmicb.2017.00543
https://doi.org/10.3389/fmicb.2017.00456
http://dx.doi.org/10.1186/s40168-017-0232-3
http://dx.doi.org/10.1111/2041-210X.12628
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Expand Up @@ -8,6 +8,12 @@

<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
<div class="figure">
<img src="http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12915-017-0402-6/MediaObjects/12915_2017_402_Fig2_HTML.gif" />

</div>
<p><a href="https://doi.org/10.1186/s12915-017-0402-6" class="uri">https://doi.org/10.1186/s12915-017-0402-6</a></p>
<hr />
<div class="figure">
<img src="https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg" />

</div>
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<link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">


![](http://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12915-017-0402-6/MediaObjects/12915_2017_402_Fig2_HTML.gif)

<https://doi.org/10.1186/s12915-017-0402-6>

----


![](https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg)

<http://dx.doi.org/10.3389/fmicb.2017.00543>
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Expand Up @@ -9,7 +9,7 @@

<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>
<p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17269/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.9.3-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-17742/total-blue.svg?style=flat" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/download-834/month-blue.svg?style=flat" /></a></p>
<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>
<div id="authors" class="section level2">
<h2><i class="fa fa-user"></i> Authors</h2>
Expand All @@ -18,7 +18,7 @@ <h2><i class="fa fa-user"></i> Authors</h2>
<div id="citation" class="section level2">
<h2><i class="fa fa-book"></i> Citation</h2>
<p>Please cite the following article when using <code>ggtree</code>:</p>
<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" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat" /></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-29-blue.svg?style=flat" alt="citation" /></a></p>
<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" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-347-blue.svg?style=flat" /></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-30-blue.svg?style=flat" alt="citation" /></a></p>
<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>
</div>
<div id="featured-articles" class="section level2">
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