1. ggtree
  2. Commit 8f72546019d05361d06ca4133f9b3ae3c9f91f0f
Browse code

add new citation

guangchuang yu authored on 14/11/2017 11:31:33
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README.md
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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-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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+[![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-21118/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--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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+[![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--14-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-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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+[![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-336-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-47-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-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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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-21118/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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docs/featured-articles/index.html
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@@ -347,7 +347,8 @@
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 <p><img src="../images/citation.png" width="880"/></p>
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 <div id="section" class="section level2">
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 <h2><i class="fa fa-calendar"></i> 2017</h2>
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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</p>
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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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 </div>
docs/featured-articles/index.xml
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@@ -19,9 +19,10 @@
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       <guid>https://guangchuangyu.github.io/ggtree/featured-articles/</guid>
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       <description>Let us know if you have published using ggtree and your publication will be featured here.
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- 2017 Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017
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+ 2017 Integrated view of Vibrio cholerae in the Americas. *Science, 2017, 358(6364):789-793.
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+Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017, 114(5):1105-111-.
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 Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus. Frontiers in Microbiology, 2017, 8:543
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-Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola. Microbiome, 2017, 5:15</description>
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+Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola.</description>
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     </item>
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   </channel>
docs/gallery/index.html
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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <div class="figure">
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+<img src="https://guangchuangyu.github.io/featured_img/ggtree/2017_science.jpg" />
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+
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+</div>
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+<p><a href="http://dx.doi.org/10.1126/science.aao2136" class="uri">http://dx.doi.org/10.1126/science.aao2136</a></p>
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+<hr />
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+<div class="figure">
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 <img src="http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif" />
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 </div>
docs/gallery/index.xml
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
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-      <description>https://doi.org/10.1186/s40168-017-0331-1
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+      <description>http://dx.doi.org/10.1126/science.aao2136
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+ https://doi.org/10.1186/s40168-017-0331-1
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  https://doi.org/10.1111/syen.12249
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  https://doi.org/10.1186/s12915-017-0402-6
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  http://dx.doi.org/10.3389/fmicb.2017.00543
docs/images/citation.png
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Binary files a/docs/images/citation.png and b/docs/images/citation.png differ
docs/index.html
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 				<h1>ggtree: visualization and annotation of phylogenetic trees </h1>
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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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-<div id="plea-to-against-bmc" class="section level2">
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+				<div id="plea-to-against-bmc" class="section level2">
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 <h2>Plea to against BMC</h2>
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 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">BMC journal protects paper of plagiarism <a href="https://t.co/FfSv7dPFXV">https://t.co/FfSv7dPFXV</a> <a href="https://twitter.com/RetractionWatch?ref_src=twsrc%5Etfw">@RetractionWatch</a> <a href="https://twitter.com/C0PE?ref_src=twsrc%5Etfw">@C0PE</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/928836702998638592?ref_src=twsrc%5Etfw">November 10, 2017</a></blockquote>
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 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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 <hr />
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+<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
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 <p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21118/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
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 <p>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>
docs/index.xml
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@@ -50,9 +50,10 @@ Sometimes I may write blog post to introduce new functions which is not availabl
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       <guid>https://guangchuangyu.github.io/ggtree/featured-articles/</guid>
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       <description>Let us know if you have published using ggtree and your publication will be featured here.
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- 2017 Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017
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+ 2017 Integrated view of Vibrio cholerae in the Americas. *Science, 2017, 358(6364):789-793.
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+Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging. PNAS, 2017, 114(5):1105-111-.
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 Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus. Frontiers in Microbiology, 2017, 8:543
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-Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola. Microbiome, 2017, 5:15</description>
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+Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in Bacteroides coprocola.</description>
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     </item>
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     <item>
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <guid>https://guangchuangyu.github.io/ggtree/gallery/</guid>
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-      <description>https://doi.org/10.1186/s40168-017-0331-1
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+      <description>http://dx.doi.org/10.1126/science.aao2136
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+ https://doi.org/10.1186/s40168-017-0331-1
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  https://doi.org/10.1111/syen.12249
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  https://doi.org/10.1186/s12915-017-0402-6
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  http://dx.doi.org/10.3389/fmicb.2017.00543
site_src/content/featured-articles/index.html
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 <p><img src="../images/citation.png" width="880"/></p>
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 <div id="section" class="section level2">
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 <h2><i class="fa fa-calendar"></i> 2017</h2>
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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</p>
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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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 </div>
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 ## <i class="fa fa-calendar"></i> 2017
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-[Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging](http://dx.doi.org/10.1073/pnas.1617959114). ***PNAS***, 2017
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+[Integrated view of *Vibrio cholerae* in the Americas](http://science.sciencemag.org/content/358/6364/789.full).
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+***Science**, 2017, 358(6364):789-793.
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+
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+
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+[Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging](http://dx.doi.org/10.1073/pnas.1617959114).
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+***PNAS***, 2017, 114(5):1105-111-.
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 [Horses in Denmark Are a Reservoir of Diverse Clones of Methicillin-Resistant and -Susceptible Staphylococcus aureus](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376617/).
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <div class="figure">
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+<img src="https://guangchuangyu.github.io/featured_img/ggtree/2017_science.jpg" />
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+
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+</div>
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+<p><a href="http://dx.doi.org/10.1126/science.aao2136" class="uri">http://dx.doi.org/10.1126/science.aao2136</a></p>
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+<hr />
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+<div class="figure">
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 <img src="http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif" />
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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+![](https://guangchuangyu.github.io/featured_img/ggtree/2017_science.jpg)
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+<http://dx.doi.org/10.1126/science.aao2136>
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+----
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 ![](http://media.springernature.com/lw785/springer-static/image/art%3A10.1186%2Fs40168-017-0331-1/MediaObjects/40168_2017_331_Fig3_HTML.gif)
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 <https://doi.org/10.1186/s40168-017-0331-1>
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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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 <div id="plea-to-against-bmc" class="section level2">
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 <h2>Plea to against BMC</h2>
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 {{% tweet "928836702998638592" %}}
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 <hr />
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+<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
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 <p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.0-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-21118/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat" alt="month" /></a></p>
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 <p>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>