1. ggtree
  2. Commit 46ee65ffb3d033f6a8976707255426c05b1a6cab
Browse code

new citation

guangchuang yu authored on 22/04/2017 05:42:54
Showing 11 changed files
README.Rmd
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@@ -69,7 +69,7 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali
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 ### Citation
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 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004", "green")`
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+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "green")`
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 ```{r echo=F, comment=NA}
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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-[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-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-14336/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.11-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-14439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/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--04--20-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--04--22-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)
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@@ -33,14 +33,14 @@ Please cite the following article when using `ggtree`:
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 ### Citation
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-[![citation](https://img.shields.io/badge/cited%20by-15-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-green.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004)
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+[![citation](https://img.shields.io/badge/cited%20by-16-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-green.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004)
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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) [![](https://img.shields.io/badge/download-14336/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/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) [![](https://img.shields.io/badge/download-14439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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          ++-------------------+------------------+-------------------+------------------+--------------+
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     3000 +                                                                                        *    +
docs/featuredArticles/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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 <p><a href="https://github.com/GuangchuangYu/featured_img">Let us know</a> if you have
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 published using <code>ggtree</code> and your publication will be featured here.</p>
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-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-15-blue.svg?style=flat" /></a>
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+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a>
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 <p><link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>
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 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>
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 <script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script>
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     height: 300px;
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   }<br />
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   </style>
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 </div>
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 <script type='text/javascript'>
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 "xkey": "year",
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 },
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 {
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  "year": 2017,
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-"cites":             14,
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 "pubid": "HtEfBTGE9r8C"
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 }
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       chartType = "Bar"
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@@ -274,6 +274,10 @@ published using <code>ggtree</code> and your publication will be featured here.<
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 <p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals
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 quantitative signatures of immune senescence and
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 aging</a>. <strong><em>PNAS</em></strong>, 2017</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
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+Methicillin-Resistant and -Susceptible Staphylococcus
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+aureus</a>.
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+<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
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 single-nucleotide polymorphism distribution in <em>Bacteroides
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 coprocola</em></a>.
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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
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 Transferases and Their Diversity in the Proximal Colon of
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 Swine</a>. <strong><em>Applied and
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-Environmental Microbiology</em></strong>. 2016,82(22):6788-6798.</p></div>
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+Environmental Microbiology</em></strong>. 2016, 82(22):6788-6798.</p></div>
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docs/gallery/index.html
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 <!-- AddToAny END -->
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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://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-15-blue.svg?style=flat" /></a></p>
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+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a></p>
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 <!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
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 <h2 id="journal-articles"><i class="fa fa-mortar-board"></i> Journal Articles</h2>
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 <ul>
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 <li><a href="http://dx.doi.org/10.1186/s40168-017-0232-3">http://dx.doi.org/10.1186/s40168-017-0232-3</a></li>
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 </ul>
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 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif" /></p>
docs/index.html
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
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 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.6.11-blue.svg?style=flat" /></a>
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-<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.7.10-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-14336/total-blue.svg?style=flat" /></a>
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+<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.7.11-blue.svg?style=flat" /></a>
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+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-14439/total-blue.svg?style=flat" /></a>
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 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1385/month-blue.svg?style=flat" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
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 grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>
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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 alt="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
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 <a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-348-blue.svg?style=flat" /></a>
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-<a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-15-blue.svg?style=flat" /></a>
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+<a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat" /></a>
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+<a href="http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&amp;customersID=RID&amp;IsProductCode=Yes&amp;product=WOS&amp;Init=Yes&amp;Func=Frame&amp;DestFail=http%3A%2F%2Fwww.webofknowledge.com&amp;action=retrieve&amp;SrcApp=RID&amp;SrcAuth=RID&amp;SID=S1i9ewwKpMcqaWLpgjp&amp;UT=WOS%3A000393305300004"><img alt="" src="https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-blue.svg?style=flat" /></a></p>
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 <p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R
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 package for visualization and annotation of phylogenetic trees with
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 their covariates and other associated data. <strong><em>Methods in Ecology and
docs/mkdocs/search_index.json
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         },
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             "location": "/featuredArticles/",
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-            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart7719fd4cfa\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             14,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart7719fd4cfa\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016,82(22):6788-6798.",
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+            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chartf981ec743\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             15,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chartf981ec743\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.",
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             "title": "Featured Articles"
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-            "text": "Phylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging .  PNAS , 2017  Gut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in  Bacteroides\ncoprocola . Microbiome , 2017, 5:15",
225 
+            "text": "Phylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging .  PNAS , 2017  Horses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus . Frontiers in Microbiology , 2017, 8:543  Gut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in  Bacteroides\ncoprocola . Microbiome , 2017, 5:15",
226 226 
             "title": " 2017"
227 227 
         },
228 228 
         {
229 229 
             "location": "/featuredArticles/#2016",
230 
-            "text": "Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine .  Applied and\nEnvironmental Microbiology . 2016,82(22):6788-6798.",
230 
+            "text": "Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine .  Applied and\nEnvironmental Microbiology . 2016, 82(22):6788-6798.",
231 231 
             "title": " 2016"
232 232 
         },
233 233 
         {
234 234 
             "location": "/gallery/",
235 
-            "text": "Journal Articles\n\n\n\n\nhttp://dx.doi.org/10.1186/s40168-017-0232-3\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1111/2041-210X.12628\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1128/AEM.02307-16\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\n\n\n Tweets\n\n\n\n\n\nAdaptive radiation of\n\n\\#Darwin\n's\nfinches showing\n\n\\#genotypic\n\nand\n\n\\#morphometric\n\nevolution. Good excuse to practice with\n\n\\#ggtree\n\n\n@guangchuangyu\n\n\npic.twitter.com/JJZ3Yje58s\n\n\n\n\u2014 Will Harvey (@_wharvey)\n\nFebruary\n15, 2017\n\n\n\n\n\n\n\n\nam quite liking\n\n\\#ggtree\n\n\n\\#rstats\n\n\n\\#ggplot\n\n\npic.twitter.com/hvywS2z4ps\n\n\n\n\u2014 Nicholas E Ilott (@IlottNick)\n\nOctober\n19, 2016\n\n\n\n\n\n\n\n\nCapital G, a reproducible logo produced by\n\n\\#ggtree\n\n\n\\#dataviz\n\n\n\\#rstats\n\n\n\\#ggplot2\n\n\npic.twitter.com/lJDcgfxAEh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nOctober\n13, 2016\n\n\n\n\n\n\n\n\nassociate tree with different type of data by\n\n\\#ggtree\n\n\nhttps://t.co/6w755VWytZ\n\n\npic.twitter.com/K8WViEi13E\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nSeptember\n7, 2016\n\n\n\n\n\n\n\n\nhow about using emoji to label host species in phylogenetic tree?\n\n\\#rstats\n\n\n\\#visualization\n\n\n\\#ggtree\n\n\n\\#emojifont\n\n\npic.twitter.com/MRKQvNNAUh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMarch\n11, 2016\n\n\n\n\n\n\n\n\n\n\\#phylomoji\n\nwith \n\\#ggtree\n\n\npic.twitter.com/yMUtm1jYF9\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nNovember\n19, 2015\n\n\n\n\n\n\n\n\nmultiple sequence alignment with\n\n\\#phylogenetic\n\ntree via\n\n\\#rstats\n pkg\n\n\\#ggtree\n.\n\npic.twitter.com/6CY57dLdeb\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n22, 2015\n\n\n\n\n\n\n\n\n\n\\#comictree\n\nvia \n\\#ggtree\n\nand \n\\#comicR\n\nin \n\\#rstats\n\n\npic.twitter.com/zwCuOQ49bq\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n15, 2015",
235 
+            "text": "Journal Articles\n\n\n\n\nhttp://dx.doi.org/10.3389/fmicb.2017.00543\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1186/s40168-017-0232-3\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1111/2041-210X.12628\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1128/AEM.02307-16\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\n\n\n Tweets\n\n\n\n\n\nAdaptive radiation of\n\n\\#Darwin\n's\nfinches showing\n\n\\#genotypic\n\nand\n\n\\#morphometric\n\nevolution. Good excuse to practice with\n\n\\#ggtree\n\n\n@guangchuangyu\n\n\npic.twitter.com/JJZ3Yje58s\n\n\n\n\u2014 Will Harvey (@_wharvey)\n\nFebruary\n15, 2017\n\n\n\n\n\n\n\n\nam quite liking\n\n\\#ggtree\n\n\n\\#rstats\n\n\n\\#ggplot\n\n\npic.twitter.com/hvywS2z4ps\n\n\n\n\u2014 Nicholas E Ilott (@IlottNick)\n\nOctober\n19, 2016\n\n\n\n\n\n\n\n\nCapital G, a reproducible logo produced by\n\n\\#ggtree\n\n\n\\#dataviz\n\n\n\\#rstats\n\n\n\\#ggplot2\n\n\npic.twitter.com/lJDcgfxAEh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nOctober\n13, 2016\n\n\n\n\n\n\n\n\nassociate tree with different type of data by\n\n\\#ggtree\n\n\nhttps://t.co/6w755VWytZ\n\n\npic.twitter.com/K8WViEi13E\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nSeptember\n7, 2016\n\n\n\n\n\n\n\n\nhow about using emoji to label host species in phylogenetic tree?\n\n\\#rstats\n\n\n\\#visualization\n\n\n\\#ggtree\n\n\n\\#emojifont\n\n\npic.twitter.com/MRKQvNNAUh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMarch\n11, 2016\n\n\n\n\n\n\n\n\n\n\\#phylomoji\n\nwith \n\\#ggtree\n\n\npic.twitter.com/yMUtm1jYF9\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nNovember\n19, 2015\n\n\n\n\n\n\n\n\nmultiple sequence alignment with\n\n\\#phylogenetic\n\ntree via\n\n\\#rstats\n pkg\n\n\\#ggtree\n.\n\npic.twitter.com/6CY57dLdeb\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n22, 2015\n\n\n\n\n\n\n\n\n\n\\#comictree\n\nvia \n\\#ggtree\n\nand \n\\#comicR\n\nin \n\\#rstats\n\n\npic.twitter.com/zwCuOQ49bq\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n15, 2015",
236 236 
             "title": "Gallery"
237 237 
         },
238 238 
         {
239 239 
             "location": "/gallery/#journal-articles",
240 
-            "text": "http://dx.doi.org/10.1186/s40168-017-0232-3      http://dx.doi.org/10.1111/2041-210X.12628      http://dx.doi.org/10.1128/AEM.02307-16      http://dx.doi.org/10.3389%2Ffcimb.2016.00036      http://dx.doi.org/10.1016/j.meegid.2015.12.006",
240 
+            "text": "http://dx.doi.org/10.3389/fmicb.2017.00543      http://dx.doi.org/10.1186/s40168-017-0232-3      http://dx.doi.org/10.1111/2041-210X.12628      http://dx.doi.org/10.1128/AEM.02307-16      http://dx.doi.org/10.3389%2Ffcimb.2016.00036      http://dx.doi.org/10.1016/j.meegid.2015.12.006",
241 241 
             "title": " Journal Articles"
242 242 
         },
243 243 
         {
mkdocs/docs/featuredArticles.md
History View file @ 46ee65ff
... ... 
@@ -24,8 +24,8 @@ output:
24 24 
 [Let us know](https://github.com/GuangchuangYu/featured_img) if you have
25 25 
 published using `ggtree` and your publication will be featured here.
26 26
27 
-[![citation](https://img.shields.io/badge/cited%20by-15-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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27 
+[![citation](https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
28 
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29 29
30 30 
 <link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>
31 31 
 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>
... ... 
@@ -40,13 +40,13 @@ published using `ggtree` and your publication will be featured here.
40 40 
     height: 300px;
41 41 
   }
42 42 
   </style>
43 
-<div id="chart7719fd4cfa" class="rChart morris">
43 
+<div id="chartf981ec743" class="rChart morris">
44 44
45 45 
 </div>
46 46
47 47 
 <script type='text/javascript'>
48 48 
     var chartParams = {
49 
- "element": "chart7719fd4cfa",
49 
+ "element": "chartf981ec743",
50 50 
 "width":            800,
51 51 
 "height":            400,
52 52 
 "xkey": "year",
... ... 
@@ -61,11 +61,11 @@ published using `ggtree` and your publication will be featured here.
61 61 
 },
62 62 
 {
63 63 
  "year": 2017,
64 
-"cites":             14,
64 
+"cites":             15,
65 65 
 "pubid": "HtEfBTGE9r8C"
66 66 
 }
67 67 
 ],
68 
-"id": "chart7719fd4cfa",
68 
+"id": "chartf981ec743",
69 69 
 "labels": "cites"
70 70 
 },
71 71 
       chartType = "Bar"
... ... 
@@ -80,6 +80,11 @@ published using `ggtree` and your publication will be featured here.
80 80 
 quantitative signatures of immune senescence and
81 81 
 aging](http://dx.doi.org/10.1073/pnas.1617959114). ***PNAS***, 2017
82 82
83 
+[Horses in Denmark Are a Reservoir of Diverse Clones of
84 
+Methicillin-Resistant and -Susceptible Staphylococcus
85 
+aureus](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376617/).
86 
+***Frontiers in Microbiology***, 2017, 8:543
87 
+
83 88 
 [Gut metagenomes of type 2 diabetic patients have characteristic
84 89 
 single-nucleotide polymorphism distribution in *Bacteroides
85 90 
 coprocola*](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3).
... ... 
@@ -91,4 +96,4 @@ coprocola*](https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-
91 96 
 [Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate
92 97 
 Transferases and Their Diversity in the Proximal Colon of
93 98 
 Swine](http://aem.asm.org/content/82/22/6788.short). ***Applied and
94 
-Environmental Microbiology***. 2016,82(22):6788-6798.
99 
+Environmental Microbiology***. 2016, 82(22):6788-6798.
mkdocs/docs/gallery.md
History View file @ 46ee65ff
... ... 
@@ -21,12 +21,18 @@ output:
21 21 
 <!-- AddToAny END -->
22 22 
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
23 23
24 
-[![citation](https://img.shields.io/badge/cited%20by-15-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
24 
+[![citation](https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
25 25
26 26 
 <!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
27 27 
 <i class="fa fa-mortar-board"></i> Journal Articles
28 28 
 ---------------------------------------------------
29 29
30 
+-   <http://dx.doi.org/10.3389/fmicb.2017.00543>
31 
+
32 
+![](https://guangchuangyu.github.io/featured_img/ggtree/fmicb-08-00543-g0002.jpg)
33 
+
34 
+------------------------------------------------------------------------
35 
+
30 36 
 -   <http://dx.doi.org/10.1186/s40168-017-0232-3>
31 37
32 38 
 ![](https://guangchuangyu.github.io/featured_img/ggtree/40168_2017_232_Fig2_HTML.gif)
mkdocs/docs/index.md
History View file @ 46ee65ff
... ... 
@@ -28,8 +28,8 @@ ggtree: visualization and annotation of phylogenetic trees
28 28 
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css">
29 29
30 30 
 [![](https://img.shields.io/badge/release%20version-1.6.11-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
31 
-[![](https://img.shields.io/badge/devel%20version-1.7.10-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
32 
-[![](https://img.shields.io/badge/download-14336/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
31 
+[![](https://img.shields.io/badge/devel%20version-1.7.11-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
32 
+[![](https://img.shields.io/badge/download-14439/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
33 33 
 [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
34 34
35 35 
 The `ggtree` package extending the *ggplot2* package. It based on
... ... 
@@ -61,8 +61,8 @@ Please cite the following article when using `ggtree`:
61 61
62 62 
 [![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
63 63 
 [![](https://img.shields.io/badge/Altmetric-348-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
64 
-[![citation](https://img.shields.io/badge/cited%20by-15-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
65 
-[![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-blue.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004)
64 
+[![citation](https://img.shields.io/badge/cited%20by-16-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
65 
+[![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-blue.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004)
66 66
67 67 
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
68 68 
 package for visualization and annotation of phylogenetic trees with
mkdocs/src/featuredArticles.rmd
History View file @ 46ee65ff
... ... 
@@ -16,7 +16,7 @@ html_preview: false
16 16
17 17
18 18 
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")`
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-`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004", "blue")`
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+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "blue")`
20 20
21 21 
 `r article_citation_trend("HtEfBTGE9r8C")`
22 22
mkdocs/src/index.rmd
History View file @ 46ee65ff
... ... 
@@ -51,7 +51,8 @@ Please cite the following article when using `ggtree`:
51 51 
 `r badge_doi("10.1111/2041-210X.12628", "blue")`
52 52 
 `r badge_altmetric("10533079", "blue")`
53 53 
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+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=S1i9ewwKpMcqaWLpgjp&UT=WOS%3A000393305300004", "blue")`
55 
+
55 56
56 57 
 __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.
57 58