1. ggtree
  2. Commit 5ccecdd03b70f5a5731a79676206547e8b75cff3
Browse code

update docs

guangchuang yu authored on 28/04/2017 02:15:56
Showing 107 changed files
DESCRIPTION
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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: 5.0.1
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=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-1.8.0-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-14583/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-1.8.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.0-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) [![](https://img.shields.io/badge/download-14583/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--27-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--28-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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 ### Citation
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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--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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+[![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)
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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-16-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></p>
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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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 "pubid": "HtEfBTGE9r8C"
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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-1.8.0-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-14583/total-blue.svg?style=flat" /></a>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
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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-347-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="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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 <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
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     "docs": [
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             "location": "/",
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-            "text": "ggtree: visualization and annotation of phylogenetic trees\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n\n \n\n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nThe \nggtree\n package extending the \nggplot2\n package. It based on\ngrammar of graphics and takes all the good parts of \nggplot2\n. \nggtree\n\nis designed for not only viewing phylogenetic tree but also displaying\nannotation data on the tree. \nggtree\n is released within the\n\nBioconductor\n project and\nthe source code is hosted on\n\n\nGitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The\nUniversity of Hong Kong.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. \nMethods in Ecology and\nEvolution\n. 2017, 8(1):28-36.\n\n\n Featured Articles\n\n\n\n\n Find out more on\n\n \nFeatured\nArticles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor\npage\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages,\nplease refer to the\n\nggtree-installation\n\nwiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to\n    be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore\n    the tree visually\n\n\n\n\n Find out details and examples on\n\n\n\nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n CRAN packages\n\n\n\n\nharrietr\n: Wrangle\n    Phylogenetic Distance Matrices and Other Utilities\n\n\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of\n    lincRNAs and protein-coding genes\n\n\nLymphoSeq\n:\n    Analyze high-throughput sequencing of T and B cell receptors\n\n\nphilr\n: Phylogenetic\n    partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n:\n    Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n:\n    Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies\n    created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you have followed \nthe important guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and",
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+            "text": "ggtree: visualization and annotation of phylogenetic trees\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n\n \n\n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nThe \nggtree\n package extending the \nggplot2\n package. It based on\ngrammar of graphics and takes all the good parts of \nggplot2\n. \nggtree\n\nis designed for not only viewing phylogenetic tree but also displaying\nannotation data on the tree. \nggtree\n is released within the\n\nBioconductor\n project and\nthe source code is hosted on\n\n\nGitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The\nUniversity of Hong Kong.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. \nMethods in Ecology and\nEvolution\n. 2017, 8(1):28-36.\n\n\n Featured Articles\n\n\n\n\n Find out more on\n\n \nFeatured\nArticles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor\npage\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages,\nplease refer to the\n\nggtree-installation\n\nwiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to\n    be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore\n    the tree visually\n\n\n\n\n Find out details and examples on\n\n\n\nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n CRAN packages\n\n\n\n\nharrietr\n: Wrangle\n    Phylogenetic Distance Matrices and Other Utilities\n\n\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of\n    lincRNAs and protein-coding genes\n\n\nLymphoSeq\n:\n    Analyze high-throughput sequencing of T and B cell receptors\n\n\nphilr\n: Phylogenetic\n    partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n:\n    Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n:\n    Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies\n    created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you have followed \nthe important guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and",
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-            "text": "Please cite the following article when using  ggtree :      G Yu , DK Smith, H Zhu, Y Guan, TTY Lam * . ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data.  Methods in Ecology and\nEvolution . 2017, 8(1):28-36.",
20 
+            "text": "Please cite the following article when using  ggtree :     G Yu , DK Smith, H Zhu, Y Guan, TTY Lam * . ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data.  Methods in Ecology and\nEvolution . 2017, 8(1):28-36.",
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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\": \"chartffa45753c39\",\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\": \"chartffa45753c39\",\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.",
220 
+            "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  .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\": \"chartba8442a5d90\",\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\": \"chartba8442a5d90\",\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.",
221 221 
             "title": "Featured Articles"
222 222 
         },
223 223 
         {
docs/sitemap.xml
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4 4
5 5 
     <url>
6 6 
      <loc>https://guangchuangyu.github.io/ggtree/</loc>
7 
-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
9 9 
     </url>
10 10
... ... 
@@ -12,7 +12,7 @@
12 12
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     <url>
14 14 
      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
15 
-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
17 17 
     </url>
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... ... 
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20 20
21 21 
     <url>
22 22 
      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
25 25 
     </url>
26 26
... ... 
@@ -28,7 +28,7 @@
28 28
29 29 
     <url>
30 30 
      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
33 33 
     </url>
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... ... 
@@ -36,7 +36,7 @@
36 36
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     <url>
38 38 
      <loc>https://guangchuangyu.github.io/ggtree/gallery/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
41 41 
     </url>
42 42
... ... 
@@ -45,55 +45,55 @@
45 45
46 46 
     <url>
47 47 
      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
49 49 
      <changefreq>daily</changefreq>
50 50 
     </url>
51 51
52 52 
     <url>
53 53 
      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
57 57
58 58 
     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
61 61 
      <changefreq>daily</changefreq>
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     </url>
63 63
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     <url>
65 65 
      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
67 67 
      <changefreq>daily</changefreq>
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     </url>
69 69
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
74 74 
     </url>
75 75
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
85 85 
      <changefreq>daily</changefreq>
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     </url>
87 87
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
91 91 
      <changefreq>daily</changefreq>
92 92 
     </url>
93 93
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     <url>
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      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>
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-     <lastmod>2017-04-27</lastmod>
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+     <lastmod>2017-04-28</lastmod>
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      <changefreq>daily</changefreq>
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     </url>
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man/Date2decimal.Rd
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@@ -18,3 +18,4 @@ convert Date to decimal format, eg "2014-05-05" to "2014.34"
18 18 
 \author{
19 19 
 Guangchuang Yu
20 20 
 }
21 
+
man/GetSubtree.df.Rd
History View file @ 5ccecdd0
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@@ -17,3 +17,4 @@ list of all child node id's from starting node.
17 17 
 \description{
18 18 
 Get all children of node from df tree using breath-first.
19 19 
 }
20 
+
man/GetSubtreeUnrooted.Rd
History View file @ 5ccecdd0
... ... 
@@ -18,3 +18,4 @@ named list of subtrees with the root id of subtree and list of node id's making
18 18 
 Get all subtrees of specified node. This includes all ancestors and relatives of node and
19 19 
 return named list of subtrees.
20 20 
 }
21 
+
man/MRCA.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ Find Most Recent Common Ancestor among a vector of tips
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/NJ.Rd
History View file @ 5ccecdd0
... ... 
@@ -31,3 +31,4 @@ print(tree)
31 31 
 \author{
32 32 
 ygc
33 33 
 }
34 
+
man/add-TREEDATA.Rd
History View file @ 5ccecdd0
... ... 
@@ -30,3 +30,4 @@ p \%<+\% dd + geom_text(aes(color=place, label=label), hjust=-0.5)
30 30 
 \author{
31 31 
 Yu Guangchuang
32 32 
 }
33 
+
man/add_TREEINFO.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ update data with tree info (y coordination and panel)
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/add_colorbar.Rd
History View file @ 5ccecdd0
... ... 
@@ -29,3 +29,4 @@ add colorbar legend
29 29 
 \author{
30 30 
 Guangchuang Yu
31 31 
 }
32 
+
man/annotation_image.Rd
History View file @ 5ccecdd0
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@@ -31,3 +31,4 @@ annotation taxa with images
31 31 
 \author{
32 32 
 Guangchuang Yu
33 33 
 }
34 
+
man/apeBoot.Rd
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... ... 
@@ -20,3 +20,4 @@ merge phylo and output of boot.phylo to 'apeBootstrap' object
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/applyLayoutDaylight.Rd
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@@ -18,3 +18,4 @@ list with tree data.frame with updated layout using daylight algorithm and max_c
18 18 
 Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the
19 19 
 specified node.
20 20 
 }
21 
+
man/as.binary.Rd
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@@ -30,3 +30,4 @@ is.binary.tree(tr2)
30 30 
 \author{
31 31 
 Guangchuang Yu \url{http://ygc.name}
32 32 
 }
33 
+
man/as.data.frame.phylo.Rd
History View file @ 5ccecdd0
... ... 
@@ -27,3 +27,4 @@ convert phylo to data.frame
27 27 
 \author{
28 28 
 Yu Guangchuang
29 29 
 }
30 
+
man/as.polytomy.Rd
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@@ -22,3 +22,4 @@ collapse binary tree to polytomy by applying 'fun' to 'feature'
22 22 
 \author{
23 23 
 Guangchuang
24 24 
 }
25 
+
man/collapse.Rd
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@@ -17,9 +17,10 @@ tree view
17 17 
 \description{
18 18 
 collapse a clade
19 19 
 }
20 
-\seealso{
21 
-expand
22 
-}
23 20 
 \author{
24 21 
 Guangchuang Yu
25 22 
 }
23 
+\seealso{
24 
+expand
25 
+}
26 
+
man/decimal2Date.Rd
History View file @ 5ccecdd0
... ... 
@@ -18,3 +18,4 @@ convert decimal format to Date, eg "2014.34" to "2014-05-05"
18 18 
 \author{
19 19 
 Guangchuang Yu
20 20 
 }
21 
+
man/dotFun.Rd
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@@ -21,3 +21,4 @@ capture name of variable
21 21 
 x <- 1
22 22 
 eval(.(x)[[1]])
23 23 
 }
24 
+
man/download.phylopic.Rd
History View file @ 5ccecdd0
... ... 
@@ -24,3 +24,4 @@ download phylopic
24 24 
 \author{
25 25 
 Guangchuang Yu
26 26 
 }
27 
+
man/expand.Rd
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@@ -17,9 +17,10 @@ tree view
17 17 
 \description{
18 18 
 expand collased clade
19 19 
 }
20 
-\seealso{
21 
-collapse
22 
-}
23 20 
 \author{
24 21 
 Guangchuang Yu
25 22 
 }
23 
+\seealso{
24 
+collapse
25 
+}
26 
+
man/facet_plot.Rd
History View file @ 5ccecdd0
... ... 
@@ -28,3 +28,4 @@ plot tree associated data in an additional panel
28 28 
 \author{
29 29 
 Guangchuang Yu
30 30 
 }
31 
+
man/flip.Rd
History View file @ 5ccecdd0
... ... 
@@ -22,3 +22,4 @@ flip position of two selected branches
22 22 
 \author{
23 23 
 Guangchuang Yu
24 24 
 }
25 
+
man/fortify.Rd
History View file @ 5ccecdd0
... ... 
@@ -33,3 +33,4 @@ fortify a phylo to data.frame
33 33 
 \author{
34 34 
 Yu Guangchuang
35 35 
 }
36 
+
man/geom_aline.Rd
History View file @ 5ccecdd0
... ... 
@@ -24,3 +24,4 @@ add horizontal align lines
24 24 
 \author{
25 25 
 Yu Guangchuang
26 26 
 }
27 
+
man/geom_balance.Rd
History View file @ 5ccecdd0
... ... 
@@ -30,10 +30,11 @@ highlights the two direct descendant clades of an internal node
30 30 
 Particularly useful when studying neighboring clades. Note that balances that
31 31 
 correspond to multichotomies will not be displayed.
32 32 
 }
33 
+\author{
34 
+Justin Silverman
35 
+}
33 36 
 \references{
34 37 
 J. Silverman, et al. \emph{A phylogenetic transform enhances
35 38 
   analysis of compositional microbiota data}. (in preparation)
36 39 
 }
37 
-\author{
38 
-Justin Silverman
39 
-}
40 
+
man/geom_cladelabel.Rd
History View file @ 5ccecdd0
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@@ -48,3 +48,4 @@ annotate a clade with bar and text label
48 48 
 \author{
49 49 
 Guangchuang Yu
50 50 
 }
51 
+
man/geom_hilight.Rd
History View file @ 5ccecdd0
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@@ -27,3 +27,4 @@ layer of hilight clade with rectangle
27 27 
 \author{
28 28 
 Guangchuang Yu
29 29 
 }
30 
+
man/geom_label2.Rd
History View file @ 5ccecdd0
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@@ -45,9 +45,10 @@ label layer
45 45 
 \description{
46 46 
 geom_label2 support aes(subset) via setup_data
47 47 
 }
48 
-\seealso{
49 
-\link[ggplot2]{geom_label}
50 
-}
51 48 
 \author{
52 49 
 Guangchuang Yu
53 50 
 }
51 
+\seealso{
52 
+\link[ggplot2]{geom_label}
53 
+}
54 
+
man/geom_nodepoint.Rd
History View file @ 5ccecdd0
... ... 
@@ -31,3 +31,4 @@ add node point
31 31 
 \author{
32 32 
 Guangchuang Yu
33 33 
 }
34 
+
man/geom_point2.Rd
History View file @ 5ccecdd0
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@@ -28,9 +28,10 @@ point layer
28 28 
 \description{
29 29 
 geom_point2 support aes(subset) via setup_data
30 30 
 }
31 
-\seealso{
32 
-\link[ggplot2]{geom_point}
33 
-}
34 31 
 \author{
35 32 
 Guangchuang Yu
36 33 
 }
34 
+\seealso{
35 
+\link[ggplot2]{geom_point}
36 
+}
37 
+
man/geom_range.Rd
History View file @ 5ccecdd0
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@@ -20,3 +20,4 @@ bar of range (HPD, range etc) to present uncertainty of evolutionary inference
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/geom_rootpoint.Rd
History View file @ 5ccecdd0
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@@ -31,3 +31,4 @@ add root point
31 31 
 \author{
32 32 
 Guangchuang Yu
33 33 
 }
34 
+
man/geom_segment2.Rd
History View file @ 5ccecdd0
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@@ -33,9 +33,10 @@ add segment layer
33 33 
 \description{
34 34 
 geom_segment2 support aes(subset) via setup_data
35 35 
 }
36 
-\seealso{
37 
-\link[ggplot2]{geom_segment}
38 
-}
39 36 
 \author{
40 37 
 Guangchuang Yu
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 }
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+\seealso{
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+\link[ggplot2]{geom_segment}
41 
+}
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+
man/geom_strip.Rd
History View file @ 5ccecdd0
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@@ -51,3 +51,4 @@ annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic
51 51 
 \author{
52 52 
 Guangchuang Yu
53 53 
 }
54 
+
man/geom_taxalink.Rd
History View file @ 5ccecdd0
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@@ -26,3 +26,4 @@ link between taxa
26 26 
 \author{
27 27 
 Guangchuang Yu
28 28 
 }
29 
+
man/geom_text2.Rd
History View file @ 5ccecdd0
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@@ -40,9 +40,10 @@ text layer
40 40 
 \description{
41 41 
 geom_text2 support aes(subset) via setup_data
42 42 
 }
43 
-\seealso{
44 
-\link[ggplot2]{geom_text}
45 
-}
46 43 
 \author{
47 44 
 Guangchuang Yu
48 45 
 }
46 
+\seealso{
47 
+\link[ggplot2]{geom_text}
48 
+}
49 
+
man/geom_tiplab.Rd
History View file @ 5ccecdd0
... ... 
@@ -38,3 +38,4 @@ ggtree(tr) + geom_tiplab()
38 38 
 \author{
39 39 
 Yu Guangchuang
40 40 
 }
41 
+
man/geom_tiplab2.Rd
History View file @ 5ccecdd0
... ... 
@@ -19,9 +19,10 @@ tip label layer
19 19 
 \description{
20 20 
 add tip label for circular layout
21 21 
 }
22 
-\references{
23 
-\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
24 
-}
25 22 
 \author{
26 23 
 Guangchuang Yu
27 24 
 }
25 
+\references{
26 
+\url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
27 
+}
28 
+
man/geom_tippoint.Rd
History View file @ 5ccecdd0
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@@ -31,3 +31,4 @@ add tip point
31 31 
 \author{
32 32 
 Guangchuang Yu
33 33 
 }
34 
+
man/geom_tree.Rd
History View file @ 5ccecdd0
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@@ -27,3 +27,4 @@ add tree layer
27 27 
 \author{
28 28 
 Yu Guangchuang
29 29 
 }
30 
+
man/geom_tree2.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ add tree layer
20 20 
 \author{
21 21 
 Yu Guangchuang
22 22 
 }
23 
+
man/geom_treescale.Rd
History View file @ 5ccecdd0
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@@ -33,3 +33,4 @@ add tree scale
33 33 
 \author{
34 34 
 Guangchuang Yu
35 35 
 }
36 
+
man/get.offspring.tip.Rd
History View file @ 5ccecdd0
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@@ -20,3 +20,4 @@ extract offspring tips
20 20 
 \author{
21 21 
 ygc
22 22 
 }
23 
+
man/get.path.Rd
History View file @ 5ccecdd0
... ... 
@@ -22,3 +22,4 @@ path from start node to end node
22 22 
 \author{
23 23 
 Guangchuang Yu
24 24 
 }
25 
+
man/get.phylopic.Rd
History View file @ 5ccecdd0
... ... 
@@ -24,3 +24,4 @@ download phylopic and convert to grob object
24 24 
 \author{
25 25 
 Guangchuang Yu
26 26 
 }
27 
+
man/getChild.df.Rd
History View file @ 5ccecdd0
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@@ -17,3 +17,4 @@ list of child node ids of parent
17 17 
 \description{
18 18 
 Get list of child node id numbers of parent node
19 19 
 }
20 
+
man/getNodeAngle.df.Rd
History View file @ 5ccecdd0
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@@ -19,3 +19,4 @@ angle in range [-1, 1], i.e. degrees/180, radians/pi
19 19 
 \description{
20 20 
 Get the angle between the two nodes specified.
21 21 
 }
22 
+
man/getNodesBreadthFirst.df.Rd
History View file @ 5ccecdd0
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@@ -15,3 +15,4 @@ list of node id's in breadth-first order.
15 15 
 \description{
16 16 
 Get the nodes of tree from root in breadth-first order.
17 17 
 }
18 
+
man/getParent.df.Rd
History View file @ 5ccecdd0
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@@ -17,3 +17,4 @@ integer node id of parent
17 17 
 \description{
18 18 
 Get parent node id of child node.
19 19 
 }
20 
+
man/getSubtree.Rd
History View file @ 5ccecdd0
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@@ -17,3 +17,4 @@ list of all child node id's from starting node.
17 17 
 \description{
18 18 
 Get all children of node from tree, including start_node.
19 19 
 }
20 
+
man/getSubtreeUnrooted.df.Rd
History View file @ 5ccecdd0
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@@ -18,3 +18,4 @@ named list of subtrees with the root id of subtree and list of node id's making
18 18 
 Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree)
19 19 
 return named list of subtrees with list name as starting node id.
20 20 
 }
21 
+
man/getTreeArcAngles.Rd
History View file @ 5ccecdd0
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@@ -20,3 +20,4 @@ named list with right and left angles in range [0,2] i.e 1 = 180 degrees, 1.5 =
20 20 
 Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and
21 21 
 left (anti-clockwise angle from +ve x-axis to subtree)
22 22 
 }
23 
+
man/get_balance_position.Rd
History View file @ 5ccecdd0
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@@ -22,3 +22,4 @@ get position of balance (xmin, xmax, ymin, ymax)
22 22 
 \author{
23 23 
 Justin Silverman
24 24 
 }
25 
+
man/get_clade_position.Rd
History View file @ 5ccecdd0
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@@ -20,3 +20,4 @@ get position of clade (xmin, xmax, ymin, ymax)
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/get_heatmap_column_position.Rd
History View file @ 5ccecdd0
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@@ -21,3 +21,4 @@ for labeling column names of heatmap produced by `gheatmap` function
21 21 
 \author{
22 22 
 Guangchuang Yu
23 23 
 }
24 
+
man/get_taxa_name.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ get taxa name of a selected node (or tree if node=NULL) sorted by their position
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/ggtree-ggproto.Rd
History View file @ 5ccecdd0
... ... 
@@ -11,3 +11,4 @@ StatBalance
11 11 
 StatHilight
12 12 
 }
13 13 
 \keyword{datasets}
14 
+
man/ggtree.Rd
History View file @ 5ccecdd0
... ... 
@@ -3,9 +3,8 @@
3 3 
 \docType{package}
4 4 
 \name{ggtree}
5 5 
 \alias{ggtree}
6 
-\alias{package-ggtree}
7 6 
 \alias{ggtree-package}
8 
-\alias{ggtree}
7 
+\alias{package-ggtree}
9 8 
 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
10 9 
 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
11 10 
 \usage{
... ... 
@@ -58,3 +57,4 @@ ggtree(tr)
58 57 
 \author{
59 58 
 Yu Guangchuang
60 59 
 }
60 
+
man/gheatmap.Rd
History View file @ 5ccecdd0
... ... 
@@ -49,3 +49,4 @@ append a heatmap of a matrix to right side of phylogenetic tree
49 49 
 \author{
50 50 
 Guangchuang Yu
51 51 
 }
52 
+
man/groupClade-methods.Rd
History View file @ 5ccecdd0
... ... 
@@ -18,3 +18,4 @@
18 18 
 \description{
19 19 
 groupClade method for ggtree object
20 20 
 }
21 
+
man/groupOTU-methods.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@
20 20 
 \description{
21 21 
 groupOTU method for ggtree object
22 22 
 }
23 
+
man/gzoom-methods.Rd
History View file @ 5ccecdd0
... ... 
@@ -3,13 +3,12 @@
3 3 
 \docType{methods}
4 4 
 \name{gzoom}
5 5 
 \alias{gzoom}
6 
-\alias{gzoom}
7 
-\alias{gzoom,ggtree-method}
8 6 
 \alias{gzoom,beast-method}
9 7 
 \alias{gzoom,codeml-method}
10 
-\alias{gzoom,treedata-method}
8 
+\alias{gzoom,ggtree-method}
11 9 
 \alias{gzoom,paml_rst-method}
12 10 
 \alias{gzoom,phylo-method}
11 
+\alias{gzoom,treedata-method}
13 12 
 \title{gzoom method}
14 13 
 \usage{
15 14 
 gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)
... ... 
@@ -51,3 +50,4 @@ figure
51 50 
 \description{
52 51 
 zoom selected subtree
53 52 
 }
53 
+
man/gzoom.phylo.Rd
History View file @ 5ccecdd0
... ... 
@@ -29,3 +29,4 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
29 29 
 \author{
30 30 
 ygc
31 31 
 }
32 
+
man/identify.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ identify node by interactive click
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/inset.Rd
History View file @ 5ccecdd0
... ... 
@@ -35,3 +35,4 @@ add insets in a tree
35 35 
 \author{
36 36 
 Guangchuang Yu
37 37 
 }
38 
+
man/layoutDaylight.Rd
History View file @ 5ccecdd0
... ... 
@@ -31,3 +31,4 @@ nodes = remove tip nodes.
31 31
32 32 
 ```
33 33 
 }
34 
+
man/layoutEqualAngle.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ tree as data.frame with equal angle layout.
20 20 
 \references{
21 21 
 "Inferring Phylogenies" by Joseph Felsenstein.
22 22 
 }
23 
+
man/msaplot.Rd
History View file @ 5ccecdd0
... ... 
@@ -28,3 +28,4 @@ multiple sequence alignment with phylogenetic tree
28 28 
 \author{
29 29 
 Guangchuang Yu
30 30 
 }
31 
+
man/multiplot.Rd
History View file @ 5ccecdd0
... ... 
@@ -29,3 +29,4 @@ plot multiple ggplot objects in one page
29 29 
 \author{
30 30 
 Guangchuang Yu
31 31 
 }
32 
+
man/nodebar.Rd
History View file @ 5ccecdd0
... ... 
@@ -26,3 +26,4 @@ generate a list of bar charts for results of ancestral state reconstruction
26 26 
 \author{
27 27 
 Guangchuang Yu
28 28 
 }
29 
+
man/nodeid.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ convert tip or node label(s) to internal node number
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/nodepie.Rd
History View file @ 5ccecdd0
... ... 
@@ -24,3 +24,4 @@ generate a list of pie charts for results of ancestral stat reconstruction
24 24 
 \author{
25 25 
 Guangchuang Yu
26 26 
 }
27 
+
man/open_tree.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ open tree with specific angle
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/phylopic.Rd
History View file @ 5ccecdd0
... ... 
@@ -35,3 +35,4 @@ add phylopic layer
35 35 
 \author{
36 36 
 Guangchuang Yu
37 37 
 }
38 
+
man/pipe.Rd
History View file @ 5ccecdd0
... ... 
@@ -17,3 +17,4 @@ pipe
17 17 
 \seealso{
18 18 
 \link[magrittr]{pipe}
19 19 
 }
20 
+
man/print.beastList.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ print information of a list of beast trees
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/reroot-methods.Rd
History View file @ 5ccecdd0
... ... 
@@ -26,3 +26,4 @@ tree object
26 26 
 \description{
27 27 
 reroot a tree
28 28 
 }
29 
+
man/rescale_tree.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ rescale branch length of tree object
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/revts.Rd
History View file @ 5ccecdd0
... ... 
@@ -18,3 +18,4 @@ reverse timescle x-axis
18 18 
 \author{
19 19 
 guangchuang yu
20 20 
 }
21 
+
man/rm.singleton.newick.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ remove singleton
20 20 
 \author{
21 21 
 Guangchuang Yu \url{http://ygc.name}
22 22 
 }
23 
+
man/rotate.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ rotate 180 degree of a selected branch
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/rotateTreePoints.df.Rd
History View file @ 5ccecdd0
... ... 
@@ -21,3 +21,4 @@ updated tree data.frame with points rotated by angle
21 21 
 \description{
22 22 
 Rotate the points in a tree data.frame around a pivot node by the angle specified.
23 23 
 }
24 
+
man/rotate_tree.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ rotate circular tree
20 20 
 \author{
21 21 
 Guangchuang Yu
22 22 
 }
23 
+
man/scaleClade.Rd
History View file @ 5ccecdd0
... ... 
@@ -26,3 +26,4 @@ scale clade
26 26 
 \author{
27 27 
 Guangchuang Yu
28 28 
 }
29 
+
man/scale_color-methods.Rd
History View file @ 5ccecdd0
... ... 
@@ -4,9 +4,9 @@
4 4 
 \name{scale_color}
5 5 
 \alias{scale_color}
6 6 
 \alias{scale_color,beast-method}
7 
-\alias{scale_color,treedata-method}
8 7 
 \alias{scale_color,paml_rst-method}
9 8 
 \alias{scale_color,phylo-method}
9 
+\alias{scale_color,treedata-method}
10 10 
 \title{scale_color method}
11 11 
 \usage{
12 12 
 scale_color(object, by, ...)
... ... 
@@ -33,3 +33,4 @@ color vector
33 33 
 \description{
34 34 
 scale color by a numerical tree attribute
35 35 
 }
36 
+
man/scale_x_ggtree.Rd
History View file @ 5ccecdd0
... ... 
@@ -22,3 +22,4 @@ scale x for tree with heatmap
22 22 
 \author{
23 23 
 Guangchuang Yu
24 24 
 }
25 
+
man/stat_balance.Rd
History View file @ 5ccecdd0
... ... 
@@ -41,3 +41,4 @@ layer
41 41 
 \description{
42 42 
 stat_balance
43 43 
 }
44 
+
man/stat_hilight.Rd
History View file @ 5ccecdd0
... ... 
@@ -39,3 +39,4 @@ layer
39 39 
 \description{
40 40 
 stat_hilight
41 41 
 }
42 
+
man/subview.Rd
History View file @ 5ccecdd0
... ... 
@@ -28,3 +28,4 @@ add subview to mainview for ggplot2 objects
28 28 
 \author{
29 29 
 Guangchuang Yu
30 30 
 }
31 
+
man/theme_inset.Rd
History View file @ 5ccecdd0
... ... 
@@ -21,3 +21,4 @@ theme for inset function
21 21 
 \author{
22 22 
 Guangchuang Yu
23 23 
 }
24 
+
man/theme_transparent.Rd
History View file @ 5ccecdd0
... ... 
@@ -18,3 +18,4 @@ transparent background theme
18 18 
 \author{
19 19 
 Guangchuang Yu
20 20 
 }
21 
+
man/theme_tree.Rd
History View file @ 5ccecdd0
... ... 
@@ -27,3 +27,4 @@ ggtree(tr) + theme_tree()
27 27 
 \author{
28 28 
 Yu Guangchuang
29 29 
 }
30 
+
man/theme_tree2.Rd
History View file @ 5ccecdd0
... ... 
@@ -27,3 +27,4 @@ ggtree(tr) + theme_tree2()
27 27 
 \author{
28 28 
 Yu Guangchuang
29 29 
 }
30 
+
man/update-TREE.Rd
History View file @ 5ccecdd0
... ... 
@@ -27,3 +27,4 @@ p \%<\% rtree(30)
27 27 
 \author{
28 28 
 Yu Guangchuang
29 29 
 }
30 
+
man/viewClade.Rd
History View file @ 5ccecdd0
... ... 
@@ -22,3 +22,4 @@ view a clade of tree
22 22 
 \author{
23 23 
 Guangchuang Yu
24 24 
 }
25 
+
man/xlim_expand.Rd
History View file @ 5ccecdd0
... ... 
@@ -20,3 +20,4 @@ expand x axis limits for specific panel
20 20 
 \author{
21 21 
 guangchuang yu
22 22 
 }
23 
+
man/xlim_tree.Rd
History View file @ 5ccecdd0
... ... 
@@ -18,3 +18,4 @@ set x axis limits for Tree panel
18 18 
 \author{
19 19 
 guangchuang yu
20 20 
 }
21 
+
mkdocs/docs/featuredArticles.md
History View file @ 5ccecdd0
... ... 
@@ -25,7 +25,6 @@ output:
25 25 
 published using `ggtree` and your publication will be featured here.
26 26
27 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 
-[![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection--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)
29 28
30 29 
 <link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>
31 30 
 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>
... ... 
@@ -40,13 +39,13 @@ published using `ggtree` and your publication will be featured here.
40 39 
     height: 300px;
41 40 
   }
42 41 
   </style>
43 
-<div id="chartffa45753c39" class="rChart morris">
42 
+<div id="chartba8442a5d90" class="rChart morris">
44 43
45 44 
 </div>
46 45
47 46 
 <script type='text/javascript'>
48 47 
     var chartParams = {
49 
- "element": "chartffa45753c39",
48 
+ "element": "chartba8442a5d90",
50 49 
 "width":            800,
51 50 
 "height":            400,
52 51 
 "xkey": "year",
... ... 
@@ -65,7 +64,7 @@ published using `ggtree` and your publication will be featured here.
65 64 
 "pubid": "HtEfBTGE9r8C"
66 65 
 }
67 66 
 ],
68 
-"id": "chartffa45753c39",
67 
+"id": "chartba8442a5d90",
69 68 
 "labels": "cites"
70 69 
 },
71 70 
       chartType = "Bar"
mkdocs/docs/index.md
History View file @ 5ccecdd0
... ... 
@@ -28,7 +28,7 @@ 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-1.8.0-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
31 
-[![](https://img.shields.io/badge/devel%20version-1.7.11-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
31 
+[![](https://img.shields.io/badge/devel%20version-1.9.0-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
32 32 
 [![](https://img.shields.io/badge/download-14583/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
... ... 
@@ -62,7 +62,6 @@ Please cite the following article when using `ggtree`:
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-347-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
64 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--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 65
67 66 
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
68 67 
 package for visualization and annotation of phylogenetic trees with
mkdocs/src/featuredArticles.rmd
History View file @ 5ccecdd0
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@@ -16,7 +16,7 @@ html_preview: false
16 16
17 17
18 18 
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")`
19 
-`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")`
19 
+
20 20
21 21 
 `r article_citation_trend("HtEfBTGE9r8C")`
22 22
mkdocs/src/index.rmd
History View file @ 5ccecdd0
... ... 
@@ -51,7 +51,7 @@ 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 
 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "blue")`
54 
-`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")`
54 
+
55 55
56 56
57 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.