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update docs

guangchuang yu authored on 17/07/2017 08:38:11
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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: 5.0.1
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+RoxygenNote: 6.0.1
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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-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.2-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-16964/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![](https://img.shields.io/badge/release%20version-1.8.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.9.2-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-17163/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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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--07--17-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)
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@@ -27,26 +27,26 @@ Please cite the following article when using `ggtree`:
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 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.
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+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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 ### Citation
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-[![citation](https://img.shields.io/badge/cited%20by-25-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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+[![citation](https://img.shields.io/badge/cited%20by-26-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
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 <img src="docs/citation.png" width="890"/>
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 ### Download stats
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-16964/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-17163/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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 <img src="docs/dlstats.png" width="890"/>
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 Contributors
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 ------------
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-This project exists thanks to all the people who contribute. [\[Contribute\]](CONTRIBUTING.md). <a href="graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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+This project exists thanks to all the people who contribute. [\[Contribute\]](CONTRIBUTING.md). <a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>
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 Backers
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 -------
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Binary files a/docs/citation.png and b/docs/citation.png differ
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@@ -300,6 +300,11 @@ accession number and we want to display species name in <em>italic</em>, we can
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 use command like this:</p>
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 <pre><code>ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
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 </code></pre>
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+<p>Another example for formating all tip labels:</p>
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+<pre><code>ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)
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+</code></pre>
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+<p>see also
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+<a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM">https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM</a>.</p>
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 <h2 id="avoid-overlapping-text-labels"><i class="fa fa-angle-double-right"></i> Avoid overlapping text labels</h2>
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 <p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a>
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 package to repel overlapping text labels.</p>
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@@ -220,7 +220,7 @@
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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-22-blue.svg?style=flat" /></a></p>
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+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-26-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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 <script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script>
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@@ -234,12 +234,12 @@ published using <code>ggtree</code> and your publication will be featured here.<
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     height: 300px;
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   }<br />
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   </style>
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-<div id="chart11855a166b40" class="rChart morris"></p>
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+<div id="chart90c7785d73f" class="rChart morris"></p>
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 </div>
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 <script type='text/javascript'>
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 "width":            800,
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 "xkey": "year",
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 },
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 {
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  "year": 2017,
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-"cites":             21,
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+"cites":             25,
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 "pubid": "HtEfBTGE9r8C" 
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 } 
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 ],
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       chartType = "Bar"
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 <!-- AddToAny END -->
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 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat" /></a></p>
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+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-26-blue.svg?style=flat" /></a></p>
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 <!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
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 <h2 id="journal-articles"><i class="fa fa-mortar-board"></i> Journal Articles</h2>
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 <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-1.8.1-blue.svg?style=flat" /></a>
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-<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.1-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-16674/total-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1117/month-blue.svg?style=flat" /></a></p>
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+<a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.2-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-17163/total-blue.svg?style=flat" /></a>
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+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-885/month-blue.svg?style=flat" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
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 grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>
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 is designed for not only viewing phylogenetic tree but also displaying
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 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
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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://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat" /></a></p>
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+<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-349-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-26-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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         }, 
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         {
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             "location": "/faq/", 
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-            "text": "Installation\n\n\n Could not find function\n\n\nIf you got \nthis\nerror\n, please make\nsure you are using the latest R and \nggtree\n.\n\n\nPackages in Bioconductor, like \nggtree\n, have different release policy\ncompare to CRAN. There are two branches, release and devel, in parallel.\nRelease branch is more stable and only document improvement and bug\nfixes will commit to it. New functions will only commit to \ndevel\n\nbranch.\n\n\nSometimes I may write blog post to introduce new functions which is not\navailable in \nrelease\n branch, you need to install the \ndevel\n version\nof \nggtree\n in order to use these new functions.\n\n\nYou can download the \ndevel\n version of \nggtree\n from\n\nhttp://bioconductor.org/packages/devel/bioc/html/ggtree.html\n and\ninstall it, or install the github version of \nggtree\n.\n\n\nThis also applied to other of my packages, including \nGOSemSim\n, \nDOSE\n,\n\nclusterProfiler\n, \nReactomePA\n and \nChIPseeker\n. If you got the\n\ncould not find function\n error, upgrade your installation to latest\nrelease. If the error still exists after upgrading to latest release,\nyou need to install the devel version.\n\n\n Text \n Label\n\n\n Tip label truncated\n\n\nggplot2 can't auto adjust xlim based on added text.\n\n\nlibrary(ggtree)\n## example tree from https://support.bioconductor.org/p/72398/\ntree\n-read.tree(text=\n(Organism1.006G249400.1:0.03977,(Organism2.022118m:0.01337,(Organism3.J34265.1:0.00284,Organism4.G02633.1:0.00468)0.51:0.0104):0.02469);\n)\nggtree(tree) + geom_tiplab()\n\n\n\n\nThis is because the units are in two different spaces (data and pixel).\nUsers can use xlim to allocate more space for tip label.\n\n\nggtree(tree) + geom_tiplab() + xlim(0, 0.06)\n\n\n\n\n Modify (tip) labels\n\n\nThis could be easily done via the \n%\n+%\n operator to attach the modified\nversion of the labels and than use \ngeom_tiplab\n to display the modified\nversion.\n\n\nraxml_file \n- system.file(\"extdata/RAxML\", \"RAxML_bipartitionsBranchLabels.H3\", package=\"ggtree\")\nraxml \n- read.raxml(raxml_file)\n\nlb = get.tree(raxml)$tip.label\nd = data.frame(label=lb, label2 = paste(\"AA\", substring(lb, 1, 5)))\nggtree(raxml) %\n+% d + geom_tiplab(aes(label=label2))\n\n\n\nsee also\n\n1\n\nand \n2\n.\n\n\n Formatting (tip) labels\n\n\nIf you want to format labels, you need to set \nparse=TRUE\n in\n\ngeom_text\n/\ngeom_tiplab\n and the \nlabel\n should be string that can be\nparsed into expression and displayed as described in \n?plotmath\n.\n\n\nFor example, the tiplabels contains two parts, species name and\naccession number and we want to display species name in \nitalic\n, we can\nuse command like this:\n\n\nggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic(\"species name\"), \"accession number\")', parse=T)\n\n\n\n Avoid overlapping text labels\n\n\nUser can use \nggrepel\n\npackage to repel overlapping text labels.\n\n\nFor example:\n\n\nlibrary(ggrepel)\nlibrary(ggtree)\nraxml_file \n- system.file(\nextdata/RAxML\n, \nRAxML_bipartitionsBranchLabels.H3\n, package=\nggtree\n)\nraxml \n- read.raxml(raxml_file)\nggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))\n\n\n\n\nFor details, please refer to \nggrepel usage\nexamples\n.\n\n\n bootstrap values from newick format\n\n\nIt's quite command to store \nbootstrap\n value as node label in \nnewick\n\nformat. Visualizing node label is easy using\n\ngeom_text2(aes(subset = !isTip, label=label))\n.\n\n\nIf you want to only display a subset of \nbootstrap\n (e.g. bootstrap \n\n80), you can't simply using\n\ngeom_text2(subset= (label \n 80), label=label)\n since \nlabel\n is a\ncharacter vector, which contains node label (bootstrap value) and tip\nlabel (taxa name). If we use\n\ngeom_text2(subset=(as.numeric(label) \n 80), label=label)\n, it will also\nfail since \nNAs\n were introduced by coercion. We need to convert \nNAs\n\nto logical \nFALSE\n, this can be done by the following code:\n\n\nnwk \n- system.file(\nextdata/RAxML\n,\nRAxML_bipartitions.H3\n, package='ggtree')\ntr \n- read.tree(nwk)\nggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) \n as.numeric(label) \n 80))\n\n\n\n\nAnother solution is converting the bootstrap value outside \nggtree\n as I\nrecommended in \ngoogle\ngroup\n.\n\n\nq \n- ggtree(tr)\nd \n- q$data\nd \n- d[!d$isTip,]\nd$label \n- as.numeric(d$label)\nd \n- d[d$label \n 80,]\n\nq + geom_text(data=d, aes(label=label))\n\n\n\n\n \naesthetic\n mapping\n\n\n inherit \naes\n\n\nggtree(rtree(30)) + geom_point()\n\n\n\n\nFor example, we can add symbolic points to nodes with \ngeom_point()\n\ndirectly. The magic here is we don't need to map \nx\n and \ny\n position of\nthe points by providing \naes(x, y)\n to \ngeom_point()\n since it was\nalready mapped by \nggtree\n function and it serves as a global mapping\nfor all layers.\n\n\nBut what if we provide a \ndataset\n in a layer and the \ndataset\n doesn't\ncontain column of \nx\n and/or \ny\n, the layer function also try to map \nx\n\nand \ny\n and also others if you map them in \nggtree\n function. As these\nvariable is not available in your \ndataset\n, you will get the following\nerror:\n\n\nError in eval(expr, envir, enclos) : object 'x' not found\n\n\n\nThis can be fixed by using parameter \ninherit.aes=FALSE\n which will\ndisable inheriting mapping from \nggtree\n function.\n\n\n use \n$\n in aes\n\n\nNEVER DO THIS.\n\n\nsee the explaination in the \nggplot2 book\n2ed\n:\n\n\n\n\nNever refer to a variable with \n$\n (e.g., \ndiamonds$carat\n) in\n\naes()\n. This breaks containment, so that the plot no longer contains\neverything it needs, and causes problems if ggplot2 changes the order\nof the rows, as it does when facetting.\n\n\n\n\nsee also\n\n1\n\nand \n2\n.\n\n\n Annotation\n\n\n colouring edges by user data\n\n\nsee my blog post: \nEdge coloring with user\ndata\n\nand also my answer on\n\nhttps://github.com/GuangchuangYu/ggtree/issues/76\n and\n\nhttps://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8\n.", 
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+            "text": "Installation\n\n\n Could not find function\n\n\nIf you got \nthis\nerror\n, please make\nsure you are using the latest R and \nggtree\n.\n\n\nPackages in Bioconductor, like \nggtree\n, have different release policy\ncompare to CRAN. There are two branches, release and devel, in parallel.\nRelease branch is more stable and only document improvement and bug\nfixes will commit to it. New functions will only commit to \ndevel\n\nbranch.\n\n\nSometimes I may write blog post to introduce new functions which is not\navailable in \nrelease\n branch, you need to install the \ndevel\n version\nof \nggtree\n in order to use these new functions.\n\n\nYou can download the \ndevel\n version of \nggtree\n from\n\nhttp://bioconductor.org/packages/devel/bioc/html/ggtree.html\n and\ninstall it, or install the github version of \nggtree\n.\n\n\nThis also applied to other of my packages, including \nGOSemSim\n, \nDOSE\n,\n\nclusterProfiler\n, \nReactomePA\n and \nChIPseeker\n. If you got the\n\ncould not find function\n error, upgrade your installation to latest\nrelease. If the error still exists after upgrading to latest release,\nyou need to install the devel version.\n\n\n Text \n Label\n\n\n Tip label truncated\n\n\nggplot2 can't auto adjust xlim based on added text.\n\n\nlibrary(ggtree)\n## example tree from https://support.bioconductor.org/p/72398/\ntree\n-read.tree(text=\n(Organism1.006G249400.1:0.03977,(Organism2.022118m:0.01337,(Organism3.J34265.1:0.00284,Organism4.G02633.1:0.00468)0.51:0.0104):0.02469);\n)\nggtree(tree) + geom_tiplab()\n\n\n\n\nThis is because the units are in two different spaces (data and pixel).\nUsers can use xlim to allocate more space for tip label.\n\n\nggtree(tree) + geom_tiplab() + xlim(0, 0.06)\n\n\n\n\n Modify (tip) labels\n\n\nThis could be easily done via the \n%\n+%\n operator to attach the modified\nversion of the labels and than use \ngeom_tiplab\n to display the modified\nversion.\n\n\nraxml_file \n- system.file(\"extdata/RAxML\", \"RAxML_bipartitionsBranchLabels.H3\", package=\"ggtree\")\nraxml \n- read.raxml(raxml_file)\n\nlb = get.tree(raxml)$tip.label\nd = data.frame(label=lb, label2 = paste(\"AA\", substring(lb, 1, 5)))\nggtree(raxml) %\n+% d + geom_tiplab(aes(label=label2))\n\n\n\nsee also\n\n1\n\nand \n2\n.\n\n\n Formatting (tip) labels\n\n\nIf you want to format labels, you need to set \nparse=TRUE\n in\n\ngeom_text\n/\ngeom_tiplab\n and the \nlabel\n should be string that can be\nparsed into expression and displayed as described in \n?plotmath\n.\n\n\nFor example, the tiplabels contains two parts, species name and\naccession number and we want to display species name in \nitalic\n, we can\nuse command like this:\n\n\nggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic(\"species name\"), \"accession number\")', parse=T)\n\n\n\nAnother example for formating all tip labels:\n\n\nggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)\n\n\n\nsee also\n\nhttps://groups.google.com/forum/?utm_medium=email\nutm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM\n.\n\n\n Avoid overlapping text labels\n\n\nUser can use \nggrepel\n\npackage to repel overlapping text labels.\n\n\nFor example:\n\n\nlibrary(ggrepel)\nlibrary(ggtree)\nraxml_file \n- system.file(\nextdata/RAxML\n, \nRAxML_bipartitionsBranchLabels.H3\n, package=\nggtree\n)\nraxml \n- read.raxml(raxml_file)\nggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))\n\n\n\n\nFor details, please refer to \nggrepel usage\nexamples\n.\n\n\n bootstrap values from newick format\n\n\nIt's quite command to store \nbootstrap\n value as node label in \nnewick\n\nformat. Visualizing node label is easy using\n\ngeom_text2(aes(subset = !isTip, label=label))\n.\n\n\nIf you want to only display a subset of \nbootstrap\n (e.g. bootstrap \n\n80), you can't simply using\n\ngeom_text2(subset= (label \n 80), label=label)\n since \nlabel\n is a\ncharacter vector, which contains node label (bootstrap value) and tip\nlabel (taxa name). If we use\n\ngeom_text2(subset=(as.numeric(label) \n 80), label=label)\n, it will also\nfail since \nNAs\n were introduced by coercion. We need to convert \nNAs\n\nto logical \nFALSE\n, this can be done by the following code:\n\n\nnwk \n- system.file(\nextdata/RAxML\n,\nRAxML_bipartitions.H3\n, package='ggtree')\ntr \n- read.tree(nwk)\nggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) \n as.numeric(label) \n 80))\n\n\n\n\nAnother solution is converting the bootstrap value outside \nggtree\n as I\nrecommended in \ngoogle\ngroup\n.\n\n\nq \n- ggtree(tr)\nd \n- q$data\nd \n- d[!d$isTip,]\nd$label \n- as.numeric(d$label)\nd \n- d[d$label \n 80,]\n\nq + geom_text(data=d, aes(label=label))\n\n\n\n\n \naesthetic\n mapping\n\n\n inherit \naes\n\n\nggtree(rtree(30)) + geom_point()\n\n\n\n\nFor example, we can add symbolic points to nodes with \ngeom_point()\n\ndirectly. The magic here is we don't need to map \nx\n and \ny\n position of\nthe points by providing \naes(x, y)\n to \ngeom_point()\n since it was\nalready mapped by \nggtree\n function and it serves as a global mapping\nfor all layers.\n\n\nBut what if we provide a \ndataset\n in a layer and the \ndataset\n doesn't\ncontain column of \nx\n and/or \ny\n, the layer function also try to map \nx\n\nand \ny\n and also others if you map them in \nggtree\n function. As these\nvariable is not available in your \ndataset\n, you will get the following\nerror:\n\n\nError in eval(expr, envir, enclos) : object 'x' not found\n\n\n\nThis can be fixed by using parameter \ninherit.aes=FALSE\n which will\ndisable inheriting mapping from \nggtree\n function.\n\n\n use \n$\n in aes\n\n\nNEVER DO THIS.\n\n\nsee the explaination in the \nggplot2 book\n2ed\n:\n\n\n\n\nNever refer to a variable with \n$\n (e.g., \ndiamonds$carat\n) in\n\naes()\n. This breaks containment, so that the plot no longer contains\neverything it needs, and causes problems if ggplot2 changes the order\nof the rows, as it does when facetting.\n\n\n\n\nsee also\n\n1\n\nand \n2\n.\n\n\n Annotation\n\n\n colouring edges by user data\n\n\nsee my blog post: \nEdge coloring with user\ndata\n\nand also my answer on\n\nhttps://github.com/GuangchuangYu/ggtree/issues/76\n and\n\nhttps://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8\n.", 
151 151
             "title": "FAQ"
152 152
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177 177
         }, 
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         {
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             "location": "/faq/#formatting-tip-labels", 
180
-            "text": "If you want to format labels, you need to set  parse=TRUE  in geom_text / geom_tiplab  and the  label  should be string that can be\nparsed into expression and displayed as described in  ?plotmath .  For example, the tiplabels contains two parts, species name and\naccession number and we want to display species name in  italic , we can\nuse command like this:  ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic(\"species name\"), \"accession number\")', parse=T)", 
180
+            "text": "If you want to format labels, you need to set  parse=TRUE  in geom_text / geom_tiplab  and the  label  should be string that can be\nparsed into expression and displayed as described in  ?plotmath .  For example, the tiplabels contains two parts, species name and\naccession number and we want to display species name in  italic , we can\nuse command like this:  ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic(\"species name\"), \"accession number\")', parse=T)  Another example for formating all tip labels:  ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)  see also https://groups.google.com/forum/?utm_medium=email utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM .", 
181 181
             "title": " Formatting (tip) labels"
182 182
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183 183
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217 217
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         {
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             "location": "/featuredArticles/", 
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\": \"chart11855a166b40\",\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\":             21,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart11855a166b40\",\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\": \"chart90c7785d73f\",\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\":             25,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart90c7785d73f\",\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
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      <loc>https://guangchuangyu.github.io/ggtree/</loc>
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 \author{
19 19
 Guangchuang Yu
20 20
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17 17
 \description{
18 18
 Get all children of node from df tree using breath-first.
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18 18
 Get all subtrees of specified node. This includes all ancestors and relatives of node and
19 19
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20 20
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20 20
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 ygc
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20 20
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21 21
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22 22
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18 18
 Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the
19 19
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20 20
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30 30
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28 28
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17 17
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18 18
 collapse a clade
19 19
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23 20
 \seealso{
24 21
 expand
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24
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25
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19 19
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25 25
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18 18
 expand collased clade
19 19
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24 21
 collapse
25 22
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24
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28 28
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29 29
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30 30
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22 22
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23 23
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24 24
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33 33
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34 34
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35 35
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25 25
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26 26
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30 30
 Particularly useful when studying neighboring clades. Note that balances that
31 31
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32 32
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33
-\author{
34
-Justin Silverman
35
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36 33
 \references{
37 34
 J. Silverman, et al. \emph{A phylogenetic transform enhances
38 35
   analysis of compositional microbiota data}. (in preparation)
39 36
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38
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49 49
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50 50
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27 27
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28 28
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29 29
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30
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47 47
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48
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53 50
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33 33
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28 28
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29 29
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30 30
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35 32
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36 33
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+\author{
35
+Guangchuang Yu
36
+}
... ...
@@ -20,4 +20,3 @@ bar of range (HPD, range etc) to present uncertainty of evolutionary inference
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -31,4 +31,3 @@ add root point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
-
... ...
@@ -33,10 +33,9 @@ add segment layer
33 33
 \description{
34 34
 geom_segment2 support aes(subset) via setup_data
35 35
 }
36
-\author{
37
-Guangchuang Yu
38
-}
39 36
 \seealso{
40 37
 \link[ggplot2]{geom_segment}
41 38
 }
42
-
39
+\author{
40
+Guangchuang Yu
41
+}
... ...
@@ -51,4 +51,3 @@ annotate associated taxa (from taxa1 to taxa2, can be Monophyletic, Polyphyletic
51 51
 \author{
52 52
 Guangchuang Yu
53 53
 }
54
-
... ...
@@ -26,4 +26,3 @@ link between taxa
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
-
... ...
@@ -40,10 +40,9 @@ text layer
40 40
 \description{
41 41
 geom_text2 support aes(subset) via setup_data
42 42
 }
43
-\author{
44
-Guangchuang Yu
45
-}
46 43
 \seealso{
47 44
 \link[ggplot2]{geom_text}
48 45
 }
49
-
46
+\author{
47
+Guangchuang Yu
48
+}
... ...
@@ -38,4 +38,3 @@ ggtree(tr) + geom_tiplab()
38 38
 \author{
39 39
 Yu Guangchuang
40 40
 }
41
-
... ...
@@ -19,10 +19,9 @@ tip label layer
19 19
 \description{
20 20
 add tip label for circular layout
21 21
 }
22
-\author{
23
-Guangchuang Yu
24
-}
25 22
 \references{
26 23
 \url{https://groups.google.com/forum/#!topic/bioc-ggtree/o35PV3iHO-0}
27 24
 }
28
-
25
+\author{
26
+Guangchuang Yu
27
+}
... ...
@@ -31,4 +31,3 @@ add tip point
31 31
 \author{
32 32
 Guangchuang Yu
33 33
 }
34
-
... ...
@@ -27,4 +27,3 @@ add tree layer
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -20,4 +20,3 @@ add tree layer
20 20
 \author{
21 21
 Yu Guangchuang
22 22
 }
23
-
... ...
@@ -33,4 +33,3 @@ add tree scale
33 33
 \author{
34 34
 Guangchuang Yu
35 35
 }
36
-
... ...
@@ -20,4 +20,3 @@ extract offspring tips
20 20
 \author{
21 21
 ygc
22 22
 }
23
-
... ...
@@ -22,4 +22,3 @@ path from start node to end node
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -24,4 +24,3 @@ download phylopic and convert to grob object
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
-
... ...
@@ -17,4 +17,3 @@ 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
-
... ...
@@ -19,4 +19,3 @@ 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
-
... ...
@@ -15,4 +15,3 @@ 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
-
... ...
@@ -17,4 +17,3 @@ integer node id of parent
17 17
 \description{
18 18
 Get parent node id of child node.
19 19
 }
20
-
... ...
@@ -17,4 +17,3 @@ 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
-
... ...
@@ -18,4 +18,3 @@ 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
-
... ...
@@ -20,4 +20,3 @@ 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
-
... ...
@@ -22,4 +22,3 @@ get position of balance (xmin, xmax, ymin, ymax)
22 22
 \author{
23 23
 Justin Silverman
24 24
 }
25
-
... ...
@@ -20,4 +20,3 @@ get position of clade (xmin, xmax, ymin, ymax)
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -21,4 +21,3 @@ for labeling column names of heatmap produced by `gheatmap` function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
-
... ...
@@ -20,4 +20,3 @@ 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
-
... ...
@@ -11,4 +11,3 @@ StatBalance
11 11
 StatHilight
12 12
 }
13 13
 \keyword{datasets}
14
-
... ...
@@ -3,8 +3,9 @@
3 3
 \docType{package}
4 4
 \name{ggtree}
5 5
 \alias{ggtree}
6
-\alias{ggtree-package}
7 6
 \alias{package-ggtree}
7
+\alias{ggtree-package}
8
+\alias{ggtree}
8 9
 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
9 10
 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
10 11
 \usage{
... ...
@@ -57,4 +58,3 @@ ggtree(tr)
57 58
 \author{
58 59
 Yu Guangchuang
59 60
 }
60
-
... ...
@@ -49,4 +49,3 @@ append a heatmap of a matrix to right side of phylogenetic tree
49 49
 \author{
50 50
 Guangchuang Yu
51 51
 }
52
-
... ...
@@ -18,4 +18,3 @@
18 18
 \description{
19 19
 groupClade method for ggtree object
20 20
 }
21
-
... ...
@@ -20,4 +20,3 @@
20 20
 \description{
21 21
 groupOTU method for ggtree object
22 22
 }
23
-
... ...
@@ -3,12 +3,13 @@
3 3
 \docType{methods}
4 4
 \name{gzoom}
5 5
 \alias{gzoom}
6
+\alias{gzoom}
7
+\alias{gzoom,ggtree-method}
6 8
 \alias{gzoom,beast-method}
7 9
 \alias{gzoom,codeml-method}
8
-\alias{gzoom,ggtree-method}
10
+\alias{gzoom,treedata-method}
9 11
 \alias{gzoom,paml_rst-method}
10 12
 \alias{gzoom,phylo-method}
11
-\alias{gzoom,treedata-method}
12 13
 \title{gzoom method}
13 14
 \usage{
14 15
 gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)
... ...
@@ -50,4 +51,3 @@ figure
50 51
 \description{
51 52
 zoom selected subtree
52 53
 }
53
-
... ...
@@ -29,4 +29,3 @@ gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
29 29
 \author{
30 30
 ygc
31 31
 }
32
-
... ...
@@ -20,4 +20,3 @@ identify node by interactive click
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -35,4 +35,3 @@ add insets in a tree
35 35
 \author{
36 36
 Guangchuang Yu
37 37
 }
38
-
... ...
@@ -31,4 +31,3 @@ nodes = remove tip nodes.
31 31
 
32 32
 ```
33 33
 }
34
-
... ...
@@ -20,4 +20,3 @@ tree as data.frame with equal angle layout.
20 20
 \references{
21 21
 "Inferring Phylogenies" by Joseph Felsenstein.
22 22
 }
23
-
... ...
@@ -28,4 +28,3 @@ multiple sequence alignment with phylogenetic tree
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
-
... ...
@@ -29,4 +29,3 @@ plot multiple ggplot objects in one page
29 29
 \author{
30 30
 Guangchuang Yu
31 31
 }
32
-
... ...
@@ -26,4 +26,3 @@ generate a list of bar charts for results of ancestral state reconstruction
26 26
 \author{
27 27
 Guangchuang Yu
28 28
 }
29
-
... ...
@@ -20,4 +20,3 @@ convert tip or node label(s) to internal node number
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -24,4 +24,3 @@ generate a list of pie charts for results of ancestral stat reconstruction
24 24
 \author{
25 25
 Guangchuang Yu
26 26
 }
27
-
... ...
@@ -20,4 +20,3 @@ open tree with specific angle
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -35,4 +35,3 @@ add phylopic layer
35 35
 \author{
36 36
 Guangchuang Yu
37 37
 }
38
-
... ...
@@ -17,4 +17,3 @@ pipe
17 17
 \seealso{
18 18
 \link[magrittr]{pipe}
19 19
 }
20
-
... ...
@@ -20,4 +20,3 @@ print information of a list of beast trees
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -26,4 +26,3 @@ tree object
26 26
 \description{
27 27
 reroot a tree
28 28
 }
29
-
... ...
@@ -20,4 +20,3 @@ rescale branch length of tree object
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -18,4 +18,3 @@ reverse timescle x-axis
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
-
... ...
@@ -20,4 +20,3 @@ remove singleton
20 20
 \author{
21 21
 Guangchuang Yu \url{http://ygc.name}
22 22
 }
23
-
... ...
@@ -20,4 +20,3 @@ rotate 180 degree of a selected branch
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -21,4 +21,3 @@ 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
-
... ...
@@ -20,4 +20,3 @@ rotate circular tree
20 20
 \author{
21 21
 Guangchuang Yu
22 22
 }
23
-
... ...
@@ -26,4 +26,3 @@ 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}
7 8
 \alias{scale_color,paml_rst-method}
8 9
 \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, ...)
... ...
@@ -33,4 +33,3 @@ color vector
33 33
 \description{
34 34
 scale color by a numerical tree attribute
35 35
 }
36
-
... ...
@@ -22,4 +22,3 @@ scale x for tree with heatmap
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -41,4 +41,3 @@ layer
41 41
 \description{
42 42
 stat_balance
43 43
 }
44
-
... ...
@@ -39,4 +39,3 @@ layer
39 39
 \description{
40 40
 stat_hilight
41 41
 }
42
-
... ...
@@ -28,4 +28,3 @@ add subview to mainview for ggplot2 objects
28 28
 \author{
29 29
 Guangchuang Yu
30 30
 }
31
-
... ...
@@ -21,4 +21,3 @@ theme for inset function
21 21
 \author{
22 22
 Guangchuang Yu
23 23
 }
24
-
... ...
@@ -18,4 +18,3 @@ transparent background theme
18 18
 \author{
19 19
 Guangchuang Yu
20 20
 }
21
-
... ...
@@ -27,4 +27,3 @@ ggtree(tr) + theme_tree()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -27,4 +27,3 @@ ggtree(tr) + theme_tree2()
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -27,4 +27,3 @@ p \%<\% rtree(30)
27 27
 \author{
28 28
 Yu Guangchuang
29 29
 }
30
-
... ...
@@ -22,4 +22,3 @@ view a clade of tree
22 22
 \author{
23 23
 Guangchuang Yu
24 24
 }
25
-
... ...
@@ -20,4 +20,3 @@ expand x axis limits for specific panel
20 20
 \author{
21 21
 guangchuang yu
22 22
 }
23
-
... ...
@@ -18,4 +18,3 @@ set x axis limits for Tree panel
18 18
 \author{
19 19
 guangchuang yu
20 20
 }
21
-
... ...
@@ -104,6 +104,13 @@ use command like this:
104 104
 
105 105
     ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
106 106
 
107
+Another example for formating all tip labels:
108
+
109
+    ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)
110
+
111
+see also
112
+<https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM>.
113
+
107 114
 <i class="fa fa-angle-double-right"></i> Avoid overlapping text labels
108 115
 ----------------------------------------------------------------------
109 116
 
... ...
@@ -24,7 +24,7 @@ output:
24 24
 [Let us know](https://github.com/GuangchuangYu/featured_img) if you have
25 25
 published using `ggtree` and your publication will be featured here.
26 26
 
27
-[![citation](https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
27
+[![citation](https://img.shields.io/badge/cited%20by-26-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
28 28
 
29 29
 <link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>
30 30
 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>
... ...
@@ -39,13 +39,13 @@ published using `ggtree` and your publication will be featured here.
39 39
     height: 300px;
40 40
   }  
41 41
   </style>
42
-<div id="chart11855a166b40" class="rChart morris">
42
+<div id="chart90c7785d73f" class="rChart morris">
43 43
 
44 44
 </div>
45 45
 
46 46
 <script type='text/javascript'>
47 47
     var chartParams = {
48
- "element": "chart11855a166b40",
48
+ "element": "chart90c7785d73f",
49 49
 "width":            800,
50 50
 "height":            400,
51 51
 "xkey": "year",
... ...
@@ -60,11 +60,11 @@ published using `ggtree` and your publication will be featured here.
60 60
 },
61 61
 {
62 62
  "year": 2017,
63
-"cites":             21,
63
+"cites":             25,
64 64
 "pubid": "HtEfBTGE9r8C" 
65 65
 } 
66 66
 ],
67
-"id": "chart11855a166b40",
67
+"id": "chart90c7785d73f",
68 68
 "labels": "cites" 
69 69
 },
70 70
       chartType = "Bar"
... ...
@@ -21,7 +21,7 @@ output:
21 21
 <!-- AddToAny END -->
22 22
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
23 23
 
24
-[![citation](https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
24
+[![citation](https://img.shields.io/badge/cited%20by-26-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
25 25
 
26 26
 <!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
27 27
 <i class="fa fa-mortar-board"></i> Journal Articles
... ...
@@ -28,9 +28,9 @@ 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-1.8.1-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)
31
-[![](https://img.shields.io/badge/devel%20version-1.9.1-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
32
-[![](https://img.shields.io/badge/download-16674/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
33
-[![](https://img.shields.io/badge/download-1117/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
31
+[![](https://img.shields.io/badge/devel%20version-1.9.2-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)
32
+[![](https://img.shields.io/badge/download-17163/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
33
+[![](https://img.shields.io/badge/download-885/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
34 34
 
35 35
 The `ggtree` package extending the *ggplot2* package. It based on
36 36
 grammar of graphics and takes all the good parts of *ggplot2*. *ggtree*
... ...
@@ -60,8 +60,8 @@ University of Hong Kong.
60 60
 Please cite the following article when using `ggtree`:
61 61
 
62 62
 [![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)
63
-[![](https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
64
-[![citation](https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
63
+[![](https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)
64
+[![citation](https://img.shields.io/badge/cited%20by-26-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)
65 65
 
66 66
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R
67 67
 package for visualization and annotation of phylogenetic trees with
... ...
@@ -76,6 +76,18 @@ For example, the tiplabels contains two parts, species name and accession number
76 76
 ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
77 77
 ```
78 78
 
79
+
80
+Another example for formating all tip labels:
81
+
82
+```
83
+ggtree(rtree(30)) + geom_tiplab(aes(label=paste0('bold(', label, ')~italic(', node, ')')), parse=TRUE)
84
+```
85
+
86
+see
87
+also
88
+<https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/BA7g-npY1BM>.
89
+
90
+
79 91
 ## <i class="fa fa-angle-double-right"></i> Avoid overlapping text labels
80 92
 
81 93
 User can use [ggrepel](https://cran.r-project.org/web/packages/ggrepel/) package to repel overlapping text labels.