Browse code

update docs

guangchuang yu authored on 28/04/2017 02:15:56
Showing 107 changed files

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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
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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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@@ -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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 <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><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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 "xkey": "year",
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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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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 <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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@@ -2,7 +2,7 @@
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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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             "title": "Home"
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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.", 
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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.", 
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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
         {
... ...
@@ -4,7 +4,7 @@
4 4
     
5 5
     <url>
6 6
      <loc>https://guangchuangyu.github.io/ggtree/</loc>
7
-     <lastmod>2017-04-27</lastmod>
7
+     <lastmod>2017-04-28</lastmod>
8 8
      <changefreq>daily</changefreq>
9 9
     </url>
10 10
     
... ...
@@ -12,7 +12,7 @@
12 12
     
13 13
     <url>
14 14
      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
15
-     <lastmod>2017-04-27</lastmod>
15
+     <lastmod>2017-04-28</lastmod>
16 16
      <changefreq>daily</changefreq>
17 17
     </url>
18 18
     
... ...
@@ -20,7 +20,7 @@
20 20
     
21 21
     <url>
22 22
      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
23
-     <lastmod>2017-04-27</lastmod>
23
+     <lastmod>2017-04-28</lastmod>
24 24
      <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>
31
-     <lastmod>2017-04-27</lastmod>
31
+     <lastmod>2017-04-28</lastmod>
32 32
      <changefreq>daily</changefreq>
33 33
     </url>
34 34
     
... ...
@@ -36,7 +36,7 @@
36 36
     
37 37
     <url>
38 38
      <loc>https://guangchuangyu.github.io/ggtree/gallery/</loc>
39
-     <lastmod>2017-04-27</lastmod>
39
+     <lastmod>2017-04-28</lastmod>
40 40
      <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>
48
-     <lastmod>2017-04-27</lastmod>
48
+     <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>
54
-     <lastmod>2017-04-27</lastmod>
54
+     <lastmod>2017-04-28</lastmod>
55 55
      <changefreq>daily</changefreq>
56 56
     </url>
57 57
         
58 58
     <url>
59 59
      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
60
-     <lastmod>2017-04-27</lastmod>
60
+     <lastmod>2017-04-28</lastmod>
61 61
      <changefreq>daily</changefreq>
62 62
     </url>
63 63
         
64 64
     <url>
65 65
      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>
66
-     <lastmod>2017-04-27</lastmod>
66
+     <lastmod>2017-04-28</lastmod>
67 67
      <changefreq>daily</changefreq>
68 68
     </url>
69 69
         
70 70
     <url>
71 71
      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
72
-     <lastmod>2017-04-27</lastmod>
72
+     <lastmod>2017-04-28</lastmod>
73 73
      <changefreq>daily</changefreq>
74 74
     </url>
75 75
         
76 76
     <url>
77 77
      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
78
-     <lastmod>2017-04-27</lastmod>
78
+     <lastmod>2017-04-28</lastmod>
79 79
      <changefreq>daily</changefreq>
80 80
     </url>
81 81
         
82 82
     <url>
83 83
      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>
84
-     <lastmod>2017-04-27</lastmod>
84
+     <lastmod>2017-04-28</lastmod>
85 85
      <changefreq>daily</changefreq>
86 86
     </url>
87 87
         
88 88
     <url>
89 89
      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
90
-     <lastmod>2017-04-27</lastmod>
90
+     <lastmod>2017-04-28</lastmod>
91 91
      <changefreq>daily</changefreq>
92 92
     </url>
93 93
         
94 94
     <url>
95 95
      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>
96
-     <lastmod>2017-04-27</lastmod>
96
+     <lastmod>2017-04-28</lastmod>
97 97
      <changefreq>daily</changefreq>
98 98
     </url>
99 99
         
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -20,3 +20,4 @@ Find Most Recent Common Ancestor among a vector of tips
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -31,3 +31,4 @@ print(tree)
31 31
 \author{
32 32
 ygc
33 33
 }
34
+
... ...
@@ -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
+
... ...
@@ -20,3 +20,4 @@ update data with tree info (y coordination and panel)
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -29,3 +29,4 @@ add colorbar legend
29 29
 \author{
30 30
 Guangchuang Yu
31 31
 }
32
+
... ...
@@ -31,3 +31,4 @@ annotation taxa with images
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
+
... ...
@@ -20,3 +20,4 @@ merge phylo and output of boot.phylo to 'apeBootstrap' object
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -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
+
... ...
@@ -30,3 +30,4 @@ is.binary.tree(tr2)
30 30
 \author{
31 31
 Guangchuang Yu \url{http://ygc.name}
32 32
 }
33
+
... ...
@@ -27,3 +27,4 @@ convert phylo to data.frame
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -22,3 +22,4 @@ collapse binary tree to polytomy by applying 'fun' to 'feature'
22 22
 \author{
23 23
 Guangchuang
24 24
 }
25
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -21,3 +21,4 @@ capture name of variable
21 21
 x <- 1
22 22
 eval(.(x)[[1]])
23 23
 }
24
+
... ...
@@ -24,3 +24,4 @@ download phylopic
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
+
... ...
@@ -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
+
... ...
@@ -28,3 +28,4 @@ plot tree associated data in an additional panel
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
+
... ...
@@ -22,3 +22,4 @@ flip position of two selected branches
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
+
... ...
@@ -33,3 +33,4 @@ fortify a phylo to data.frame
33 33
 \author{
34 34
 Yu Guangchuang
35 35
 }
36
+
... ...
@@ -24,3 +24,4 @@ add horizontal align lines
24 24
 \author{
25 25
 Yu Guangchuang
26 26
 }
27
+
... ...
@@ -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
+
... ...
@@ -48,3 +48,4 @@ annotate a clade with bar and text label
48 48
 \author{
49 49
 Guangchuang Yu
50 50
 }
51
+
... ...
@@ -27,3 +27,4 @@ layer of hilight clade with rectangle
27 27
 \author{
28 28
 Guangchuang Yu
29 29
 }
30
+
... ...
@@ -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
+
... ...
@@ -31,3 +31,4 @@ add node point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -31,3 +31,4 @@ add root point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
+
... ...
@@ -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
41 38
 }
39
+\seealso{
40
+\link[ggplot2]{geom_segment}
41
+}
42
+
... ...
@@ -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
+
... ...
@@ -26,3 +26,4 @@ link between taxa
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
+
... ...
@@ -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
+
... ...
@@ -38,3 +38,4 @@ ggtree(tr) + geom_tiplab()
38 38
 \author{
39 39
 Yu Guangchuang
40 40
 }
41
+
... ...
@@ -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
+
... ...
@@ -31,3 +31,4 @@ add tip point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
+
... ...
@@ -27,3 +27,4 @@ add tree layer
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -20,3 +20,4 @@ add tree layer
20 20
 \author{
21 21
 Yu Guangchuang
22 22
 }
23
+
... ...
@@ -33,3 +33,4 @@ add tree scale
33 33
 \author{
34 34
 Guangchuang Yu
35 35
 }
36
+
... ...
@@ -20,3 +20,4 @@ extract offspring tips
20 20
 \author{
21 21
 ygc
22 22
 }
23
+
... ...
@@ -22,3 +22,4 @@ path from start node to end node
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
+
... ...
@@ -24,3 +24,4 @@ download phylopic and convert to grob object
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -17,3 +17,4 @@ integer node id of parent
17 17
 \description{
18 18
 Get parent node id of child node.
19 19
 }
20
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -22,3 +22,4 @@ get position of balance (xmin, xmax, ymin, ymax)
22 22
 \author{
23 23
 Justin Silverman
24 24
 }
25
+
... ...
@@ -20,3 +20,4 @@ get position of clade (xmin, xmax, ymin, ymax)
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -21,3 +21,4 @@ for labeling column names of heatmap produced by `gheatmap` function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
+
... ...
@@ -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
+
... ...
@@ -11,3 +11,4 @@ StatBalance
11 11
 StatHilight
12 12
 }
13 13
 \keyword{datasets}
14
+
... ...
@@ -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
+
... ...
@@ -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
+
... ...
@@ -18,3 +18,4 @@
18 18
 \description{
19 19
 groupClade method for ggtree object
20 20
 }
21
+
... ...
@@ -20,3 +20,4 @@
20 20
 \description{
21 21
 groupOTU method for ggtree object
22 22
 }
23
+
... ...
@@ -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
+
... ...
@@ -29,3 +29,4 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
29 29
 \author{
30 30
 ygc
31 31
 }
32
+
... ...
@@ -20,3 +20,4 @@ identify node by interactive click
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -35,3 +35,4 @@ add insets in a tree
35 35
 \author{
36 36
 Guangchuang Yu
37 37
 }
38
+
... ...
@@ -31,3 +31,4 @@ nodes = remove tip nodes.
31 31
 
32 32
 ```
33 33
 }
34
+
... ...
@@ -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
+
... ...
@@ -28,3 +28,4 @@ multiple sequence alignment with phylogenetic tree
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
+
... ...
@@ -29,3 +29,4 @@ plot multiple ggplot objects in one page
29 29
 \author{
30 30
 Guangchuang Yu
31 31
 }
32
+
... ...
@@ -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
+
... ...
@@ -20,3 +20,4 @@ convert tip or node label(s) to internal node number
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -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
+
... ...
@@ -20,3 +20,4 @@ open tree with specific angle
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -35,3 +35,4 @@ add phylopic layer
35 35
 \author{
36 36
 Guangchuang Yu
37 37
 }
38
+
... ...
@@ -17,3 +17,4 @@ pipe
17 17
 \seealso{
18 18
 \link[magrittr]{pipe}
19 19
 }
20
+
... ...
@@ -20,3 +20,4 @@ print information of a list of beast trees
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -26,3 +26,4 @@ tree object
26 26
 \description{
27 27
 reroot a tree
28 28
 }
29
+
... ...
@@ -20,3 +20,4 @@ rescale branch length of tree object
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -18,3 +18,4 @@ reverse timescle x-axis
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
+
... ...
@@ -20,3 +20,4 @@ remove singleton
20 20
 \author{
21 21
 Guangchuang Yu \url{http://ygc.name}
22 22
 }
23
+
... ...
@@ -20,3 +20,4 @@ rotate 180 degree of a selected branch
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -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
+
... ...
@@ -20,3 +20,4 @@ rotate circular tree
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
+
... ...
@@ -26,3 +26,4 @@ scale clade
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
+
... ...
@@ -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
+
... ...
@@ -22,3 +22,4 @@ scale x for tree with heatmap
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
+
... ...
@@ -41,3 +41,4 @@ layer
41 41
 \description{
42 42
 stat_balance
43 43
 }
44
+
... ...
@@ -39,3 +39,4 @@ layer
39 39
 \description{
40 40
 stat_hilight
41 41
 }
42
+
... ...
@@ -28,3 +28,4 @@ add subview to mainview for ggplot2 objects
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
+
... ...
@@ -21,3 +21,4 @@ theme for inset function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
+
... ...
@@ -18,3 +18,4 @@ transparent background theme
18 18
 \author{
19 19
 Guangchuang Yu
20 20
 }
21
+
... ...
@@ -27,3 +27,4 @@ ggtree(tr) + theme_tree()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -27,3 +27,4 @@ ggtree(tr) + theme_tree2()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -27,3 +27,4 @@ p \%<\% rtree(30)
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
+
... ...
@@ -22,3 +22,4 @@ view a clade of tree
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
+
... ...
@@ -20,3 +20,4 @@ expand x axis limits for specific panel
20 20
 \author{
21 21
 guangchuang yu
22 22
 }
23
+
... ...
@@ -18,3 +18,4 @@ set x axis limits for Tree panel
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
+
... ...
@@ -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"
... ...
@@ -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
... ...
@@ -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
 
... ...
@@ -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.