1. ggtree
  2. Commit 887bd02c82e2db14ec550491a518565bf9bab0c9
Browse code

update docs

guangchuang yu authored on 15/12/2017 02:56:00
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README.md
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@@ -6,7 +6,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.3-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-22348/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/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--12--14-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
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+[![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--12--15-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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docs/documentation/index.html
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
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-<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a> <i class="fa fa-arrow-left"></i> The Molecular Ecologist</li>
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+<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a></li>
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 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
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 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
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+<li><a href="https://aschuerch.github.io/posts/2017-04-24-blog-post-1">Drawing a tree with colored tips in R (ggtree)</a></li>
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 </ul>
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 </div>
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 <div id="tree-annotation" class="section level3">
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 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
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 <ul>
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 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
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+<li><a href="https://jean.manguy.eu/post/subtrees-as-triangles-with-ggtree/">Subtrees as triangles with ggtree</a></li>
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 </ul>
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 </div>
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 <div id="application" class="section level3">
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 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
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 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
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 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
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+<li><a href="https://youtu.be/tqspAXM0UQE">R语言包ggtree 进化树绘图</a></li>
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 </ul>
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 </div>
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 <div id="workflow" class="section level2">
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 <ul>
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 <li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>
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 </ul>
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+</div>
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+<div id="workflow-1" class="section level2">
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+<h2><i class="fa fa-users"></i> Workflow</h2>
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+<ul>
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+<li><a href="https://4va.github.io/biodatasci/r-ggtree.html">Visualizing and Annotating Phylogenetic Trees with R+ggtree</a></li>
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+</ul>
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 </div>
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docs/documentation/index.xml
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <guid>https://guangchuangyu.github.io/ggtree/documentation/</guid>
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-      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist Growing a ggtree Growing a ggtree - part 2, adding tip shapes    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)   </description>
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+      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree Growing a ggtree Growing a ggtree - part 2, adding tip shapes Drawing a tree with colored tips in R (ggtree)    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree Subtrees as triangles with ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling R语言包ggtree 进化树绘图    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)    Workflow  Visualizing and Annotating Phylogenetic Trees with R+ggtree   </description>
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     </item>
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   </channel>
docs/index.html
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 				<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
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 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
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-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.3-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-22066/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat" alt="month" /></a></p>
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+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.3-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-22348/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat" alt="month" /></a></p>
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 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
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 <div id="authors" class="section level2">
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 <h2><i class="fa fa-user"></i> Authors</h2>
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 <div id="citation" class="section level2">
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 <h2><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 src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-334-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-52-blue.svg?style=flat" alt="citation" /></a></p>
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+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-325-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-55-blue.svg?style=flat" alt="citation" /></a></p>
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 <p><strong>G Yu</strong>, 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. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
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 </div>
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 <div id="featured-articles" class="section level2">
docs/index.xml
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       <pubDate>Mon, 24 Jul 2017 00:11:02 +0100</pubDate>
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       <guid>https://guangchuangyu.github.io/ggtree/documentation/</guid>
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-      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree  The Molecular Ecologist Growing a ggtree Growing a ggtree - part 2, adding tip shapes    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)   </description>
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+      <description> Vignettes  ggtree Tree Data Import Tree Visualization Tree Annotation Tree Manipulation Advance Tree Annotation ggtree utilities Phylomoji    Blog posts  News and updates  viewing and annotating phylogenetic tree with ggtree ggtree in Bioconductor 3.1 BioC 3.1: NEWS of my BioC packages BioC 3.2: NEWS of my BioC packages News of ggtree BioC 3.3: NEWS of my BioC packages BioC 3.4: NEWS of my BioC packages ggtree paper published    Data manipulation  subsetting data in ggtree ggtree supports phylip tree format convert graphic object to tree object using treeio    Tree visualization  ggtree - updating a tree view an example of drawing beast tree using ggtree Phylogenetic trees in R using ggtree Growing a ggtree Growing a ggtree - part 2, adding tip shapes Drawing a tree with colored tips in R (ggtree)    Tree annotation  label edge number in ggtree Edge coloring with user data subview Annotate a phylogenetic tree with insets ggtree annotate phylogenetic tree with local images embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function identify method for ggtree facet_plot: a general solution to associate data with phylogenetic tree align genomic features with phylogenetic tree ggjoy facet with ggtree xlim_tree: set x axis limits for only Tree panel add layer to specific panel of facet_plot output    Tree manipulation  flip and rotate branches in ggtree Subtrees as triangles with ggtree    Application  ggtree for microbiome data ggtree for outbreak data ggtree version of plotTree reproducible logo generated by ggtree    Funny stuff  ggtree with funny fonts comic phylogenetic tree with ggtree and comicR use emoji font in R     Slides  Generating publication quality figures using R &amp;amp; ggplot2 ggtree for visualization and annotation of phylogenetic trees    Video  interactive clade highlighting interactive rotating clades interactive clade labeling R语言包ggtree 进化树绘图    Workflow  recreate a tree from a publication (Bloom et al, Science 2010)    Workflow  Visualizing and Annotating Phylogenetic Trees with R+ggtree   </description>
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       <guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
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       <description>Leave me a message on
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-Also, thanks to @guangchuangyu for the R package ggtree - these visualizations are made possible by the reliability that sweet #rstats package!
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-&amp;mdash; Alex Washburne (@alex_washburne) November 30, 2017  Thank you so much @guangchuangyu! #ggtree is the easy way for my phd data analysis &amp;lt;3 love it!
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-&amp;mdash; Francisco Romero (@pinchehippie) October 17, 2017  Now on https://t.co/50tYJLLZqc - a spotlight on the Top Tools for R Programming:</description>
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+Subtrees as triangles with ggtree https://t.co/NNdur8PS2Y #rstats https://t.co/7PZbN9daHy
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+&amp;mdash; Jean 👨‍💻 (@JeanManguy) December 15, 2017  Drawing a tree with colored tips in R (ggtree)
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+https://t.co/s9FYUbynCd @guangchuangyu
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+&amp;mdash; Guanyang Zhang 张冠阳 (@GYZhang2) December 13, 2017  ggtree使ってみた。”注目する枝組み合わせの分布”みたいなものを可視化したいんだけどまだちょっと見にくい。 pic.twitter.com/w5xs7cd0jQ
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+&amp;mdash; Kenji Fukushima (@kfuku0502) December 13, 2017  ggtreeにはhttps://t.co/8T3WU8h9pWからシルエット画像を取ってくる用の関数まで用意されているのか…。HGTの描画も楽そうだし、これはもう系統樹描画に関してはETEを投げ捨ててggtreeに鞍替えするべきか。https://t.co/gynekuwjCe
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+&amp;mdash; Kenji Fukushima (@kfuku0502) December 11, 2017  I&amp;#39;ve had good experiences with ggtree https://t.co/eRLhDoc4Hm
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+&amp;mdash; Philipp Bayer (@PhilippBayer) December 7, 2017  Also, thanks to @guangchuangyu for the R package ggtree - these visualizations are made possible by the reliability that sweet #rstats package!</description>
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 			<p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
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 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
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-<p><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Also, thanks to <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> for the R package ggtree - these visualizations are made possible by the reliability that sweet <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> package!</p>&mdash; Alex Washburne (@alex_washburne) <a href="https://twitter.com/alex_washburne/status/936241103585517568?ref_src=twsrc%5Etfw">November 30, 2017</a></blockquote>
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+<p><blockquote class="twitter-tweet"><p lang="en" dir="ltr">Subtrees as triangles with ggtree <a href="https://t.co/NNdur8PS2Y">https://t.co/NNdur8PS2Y</a>  <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://t.co/7PZbN9daHy">https://t.co/7PZbN9daHy</a></p>&mdash; Jean 👨‍💻 (@JeanManguy) <a href="https://twitter.com/JeanManguy/status/941463119490150405?ref_src=twsrc%5Etfw">December 15, 2017</a></blockquote>
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+<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Drawing a tree with colored tips in R (ggtree)<br> <a href="https://t.co/s9FYUbynCd">https://t.co/s9FYUbynCd</a>  <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a></p>&mdash; Guanyang Zhang 张冠阳 (@GYZhang2) <a href="https://twitter.com/GYZhang2/status/941040327816892416?ref_src=twsrc%5Etfw">December 13, 2017</a></blockquote>
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+<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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+<blockquote class="twitter-tweet"><p lang="ja" dir="ltr">ggtree使ってみた。”注目する枝組み合わせの分布”みたいなものを可視化したいんだけどまだちょっと見にくい。 <a href="https://t.co/w5xs7cd0jQ">pic.twitter.com/w5xs7cd0jQ</a></p>&mdash; Kenji Fukushima (@kfuku0502) <a href="https://twitter.com/kfuku0502/status/940738021514547201?ref_src=twsrc%5Etfw">December 13, 2017</a></blockquote>
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+<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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+<blockquote class="twitter-tweet"><p lang="ja" dir="ltr">ggtreeには<a href="https://t.co/8T3WU8h9pW">https://t.co/8T3WU8h9pW</a>からシルエット画像を取ってくる用の関数まで用意されているのか…。HGTの描画も楽そうだし、これはもう系統樹描画に関してはETEを投げ捨ててggtreeに鞍替えするべきか。<a href="https://t.co/gynekuwjCe">https://t.co/gynekuwjCe</a></p>&mdash; Kenji Fukushima (@kfuku0502) <a href="https://twitter.com/kfuku0502/status/940337892030910467?ref_src=twsrc%5Etfw">December 11, 2017</a></blockquote>
355 
+<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
356 
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">I&#39;ve had good experiences with ggtree <a href="https://t.co/eRLhDoc4Hm">https://t.co/eRLhDoc4Hm</a></p>&mdash; Philipp Bayer (@PhilippBayer) <a href="https://twitter.com/PhilippBayer/status/938702392450617344?ref_src=twsrc%5Etfw">December 7, 2017</a></blockquote>
357 
+<script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
358 
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Also, thanks to <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> for the R package ggtree - these visualizations are made possible by the reliability that sweet <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> package!</p>&mdash; Alex Washburne (@alex_washburne) <a href="https://twitter.com/alex_washburne/status/936241103585517568?ref_src=twsrc%5Etfw">November 30, 2017</a></blockquote>
349 359 
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
350 360 
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">Thank you so much <a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a>! <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> is the easy way for my phd data analysis &lt;3 love it!</p>&mdash; Francisco Romero (@pinchehippie) <a href="https://twitter.com/pinchehippie/status/920370392451178496?ref_src=twsrc%5Etfw">October 17, 2017</a></blockquote>
351 361 
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
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@@ -403,7 +413,7 @@
403 413 
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
404 414 
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr">am quite liking <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> <a href="https://twitter.com/hashtag/ggplot?src=hash&amp;ref_src=twsrc%5Etfw">#ggplot</a> <a href="https://t.co/hvywS2z4ps">pic.twitter.com/hvywS2z4ps</a></p>&mdash; Nicholas E Ilott (@IlottNick) <a href="https://twitter.com/IlottNick/status/788751417746059264?ref_src=twsrc%5Etfw">October 19, 2016</a></blockquote>
405 415 
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
406 
-<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Treespace visualization of a heuristic best tree search in <a href="https://twitter.com/hashtag/R?src=hash&amp;ref_src=twsrc%5Etfw">#R</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/hnSJpIABql">pic.twitter.com/hnSJpIABql</a></p>&mdash; 𝓐𝖑𝖊𝖏𝖆𝖓𝖉𝖗𝖔 𝕯𝖆𝖒𝖎𝖆𝖓 𝓢𝖊𝖗𝖗𝖆𝖓𝖔 ⑂ (@antropoteuthis) <a href="https://twitter.com/antropoteuthis/status/693123105707986944?ref_src=twsrc%5Etfw">January 29, 2016</a></blockquote>
416 
+<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Treespace visualization of a heuristic best tree search in <a href="https://twitter.com/hashtag/R?src=hash&amp;ref_src=twsrc%5Etfw">#R</a> package <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> <a href="https://twitter.com/hashtag/phylogenetics?src=hash&amp;ref_src=twsrc%5Etfw">#phylogenetics</a> <a href="https://t.co/hnSJpIABql">pic.twitter.com/hnSJpIABql</a></p>&mdash; Alejandro Damian Serrano 🔬 (@antropoteuthis) <a href="https://twitter.com/antropoteuthis/status/693123105707986944?ref_src=twsrc%5Etfw">January 29, 2016</a></blockquote>
407 417 
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
408 418 
 <blockquote class="twitter-tweet"><p lang="en" dir="ltr"><a href="https://twitter.com/guangchuangyu?ref_src=twsrc%5Etfw">@guangchuangyu</a> Updated to latest <a href="https://twitter.com/hashtag/ggtree?src=hash&amp;ref_src=twsrc%5Etfw">#ggtree</a> and <a href="https://twitter.com/hashtag/ggplot2?src=hash&amp;ref_src=twsrc%5Etfw">#ggplot2</a> and very impressed! Any ideas on using geom_label with tip labels to add box/fill?</p>&mdash; Jo Williams-Newkirk (@ajwnewkirk) <a href="https://twitter.com/ajwnewkirk/status/691762302492790788?ref_src=twsrc%5Etfw">January 25, 2016</a></blockquote>
409 419 
 <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
docs/tweets/index.xml
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@@ -19,9 +19,13 @@
19 19
20 20 
       <guid>https://guangchuangyu.github.io/ggtree/tweets/</guid>
21 21 
       <description>Leave me a message on
22 
-Also, thanks to @guangchuangyu for the R package ggtree - these visualizations are made possible by the reliability that sweet #rstats package!
23 
-&amp;mdash; Alex Washburne (@alex_washburne) November 30, 2017  Thank you so much @guangchuangyu! #ggtree is the easy way for my phd data analysis &amp;lt;3 love it!
24 
-&amp;mdash; Francisco Romero (@pinchehippie) October 17, 2017  Now on https://t.co/50tYJLLZqc - a spotlight on the Top Tools for R Programming:</description>
22 
+Subtrees as triangles with ggtree https://t.co/NNdur8PS2Y #rstats https://t.co/7PZbN9daHy
23 
+&amp;mdash; Jean 👨‍💻 (@JeanManguy) December 15, 2017  Drawing a tree with colored tips in R (ggtree)
24 
+https://t.co/s9FYUbynCd @guangchuangyu
25 
+&amp;mdash; Guanyang Zhang 张冠阳 (@GYZhang2) December 13, 2017  ggtree使ってみた。”注目する枝組み合わせの分布”みたいなものを可視化したいんだけどまだちょっと見にくい。 pic.twitter.com/w5xs7cd0jQ
26 
+&amp;mdash; Kenji Fukushima (@kfuku0502) December 13, 2017  ggtreeにはhttps://t.co/8T3WU8h9pWからシルエット画像を取ってくる用の関数まで用意されているのか…。HGTの描画も楽そうだし、これはもう系統樹描画に関してはETEを投げ捨ててggtreeに鞍替えするべきか。https://t.co/gynekuwjCe
27 
+&amp;mdash; Kenji Fukushima (@kfuku0502) December 11, 2017  I&amp;#39;ve had good experiences with ggtree https://t.co/eRLhDoc4Hm
28 
+&amp;mdash; Philipp Bayer (@PhilippBayer) December 7, 2017  Also, thanks to @guangchuangyu for the R package ggtree - these visualizations are made possible by the reliability that sweet #rstats package!</description>
25 29 
     </item>
26 30
27 31 
   </channel>
site_src/content/documentation/index.html
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48 48 
 <ul>
49 49 
 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>
50 50 
 <li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>
51 
-<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a> <i class="fa fa-arrow-left"></i> The Molecular Ecologist</li>
51 
+<li><a href="http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/">Phylogenetic trees in R using ggtree</a></li>
52 52 
 <li><a href="https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration">Growing a ggtree</a></li>
53 53 
 <li><a href="https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2">Growing a ggtree - part 2, adding tip shapes</a></li>
54 
+<li><a href="https://aschuerch.github.io/posts/2017-04-24-blog-post-1">Drawing a tree with colored tips in R (ggtree)</a></li>
54 55 
 </ul>
55 56 
 </div>
56 57 
 <div id="tree-annotation" class="section level3">
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74 75 
 <h3><i class="fa fa-angle-double-right"></i> Tree manipulation</h3>
75 76 
 <ul>
76 77 
 <li><a href="https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in ggtree</a></li>
78 
+<li><a href="https://jean.manguy.eu/post/subtrees-as-triangles-with-ggtree/">Subtrees as triangles with ggtree</a></li>
77 79 
 </ul>
78 80 
 </div>
79 81 
 <div id="application" class="section level3">
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107 109 
 <li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
108 110 
 <li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
109 111 
 <li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
112 
+<li><a href="https://youtu.be/tqspAXM0UQE">R语言包ggtree 进化树绘图</a></li>
110 113 
 </ul>
111 114 
 </div>
112 115 
 <div id="workflow" class="section level2">
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115 118 
 <li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>, <strong><em>Science</em></strong> 2010)</a></li>
116 119 
 </ul>
117 120 
 </div>
121 
+<div id="workflow-1" class="section level2">
122 
+<h2><i class="fa fa-users"></i> Workflow</h2>
123 
+<ul>
124 
+<li><a href="https://4va.github.io/biodatasci/r-ggtree.html">Visualizing and Annotating Phylogenetic Trees with R+ggtree</a></li>
125 
+</ul>
126 
+</div>
site_src/content/documentation/index.rmd
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43 43
44 44 
 + [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)
45 45 
 + [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)
46 
-+ [Phylogenetic trees in R using ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/) <i class="fa fa-arrow-left"></i> The Molecular Ecologist
46 
++ [Phylogenetic trees in R using ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/)
47 47 
 + [Growing a ggtree](https://phe-bioinformatics.github.io/blog/2017/06/14/ggtree_exploration)
48 48 
 + [Growing a ggtree - part 2, adding tip shapes](https://phe-bioinformatics.github.io/blog/2017/07/07/ggtree_part2)
49 
++ [Drawing a tree with colored tips in R (ggtree)](https://aschuerch.github.io/posts/2017-04-24-blog-post-1)
49 50
50 51 
 ### <i class="fa fa-angle-double-right"></i> Tree annotation
51 52
... ... 
@@ -66,6 +67,8 @@ weight: 10
66 67 
 ### <i class="fa fa-angle-double-right"></i> Tree manipulation
67 68
68 69 
 + [flip and rotate branches in ggtree](https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree)
70 
++ [Subtrees as triangles with ggtree](https://jean.manguy.eu/post/subtrees-as-triangles-with-ggtree/)
71 
+
69 72
70 73 
 ### <i class="fa fa-angle-double-right"></i> Application
71 74
... ... 
@@ -92,7 +95,13 @@ weight: 10
92 95 
 + [interactive clade highlighting](https://www.youtube.com/watch?v=KcF8Ec38mzI)
93 96 
 + [interactive rotating clades](https://www.youtube.com/watch?v=lKNn4QlPO0E)
94 97 
 + [interactive clade labeling](https://www.youtube.com/watch?v=SmcceRD_jxg)
98 
++ [R语言包ggtree 进化树绘图](https://youtu.be/tqspAXM0UQE)
95 99
96 100 
 ## <i class="fa fa-gift"></i> Workflow
97 101
98 102 
 + [recreate a tree from a publication (__Bloom__ *et al*, __*Science*__ 2010)](https://rpubs.com/gutijosh9430/124817)
103 
+
104 
+
105 
+## <i class="fa fa-users"></i> Workflow
106 
+
107 
++ [Visualizing and Annotating Phylogenetic Trees with R+ggtree](https://4va.github.io/biodatasci/r-ggtree.html)
site_src/content/index.html
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9 9
10 10 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"> <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>
11 11 
 <p><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></p>
12 
-<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.3-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-22066/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat" alt="month" /></a></p>
12 
+<p><a href="https://bioconductor.org/packages/ggtree"><img src="https://img.shields.io/badge/release%20version-1.10.0-blue.svg?style=flat" alt="releaseVersion" /></a> <a href="https://github.com/guangchuangyu/ggtree"><img src="https://img.shields.io/badge/devel%20version-1.11.3-blue.svg?style=flat" alt="develVersion" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-22348/total-blue.svg?style=flat" alt="total" /></a> <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img src="https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat" alt="month" /></a></p>
13 13 
 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree. <em>ggtree</em> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>
14 14 
 <div id="authors" class="section level2">
15 15 
 <h2><i class="fa fa-user"></i> Authors</h2>
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18 18 
 <div id="citation" class="section level2">
19 19 
 <h2><i class="fa fa-book"></i> Citation</h2>
20 20 
 <p>Please cite the following article when using <code>ggtree</code>:</p>
21 
-<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-334-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-52-blue.svg?style=flat" alt="citation" /></a></p>
21 
+<p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" alt="doi" /></a> <a href="https://www.altmetric.com/details/10533079"><img src="https://img.shields.io/badge/Altmetric-325-blue.svg?style=flat" alt="Altmetric" /></a> <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img src="https://img.shields.io/badge/cited%20by-55-blue.svg?style=flat" alt="citation" /></a></p>
22 22 
 <p><strong>G Yu</strong>, 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. <strong><em>Methods in Ecology and Evolution</em></strong>. 2017, 8(1):28-36.</p>
23 23 
 </div>
24 24 
 <div id="featured-articles" class="section level2">
site_src/content/tweets/index.html
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9 9 
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
10 10 
 <p><font size="4"><strong>Leave me a message on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a></strong></font></p>
11 
-<p>{{% tweet "936241103585517568" %}}{{% tweet "920370392451178496" %}}{{% tweet "912971120198012929" %}}{{% tweet "907543915686793217" %}}{{% tweet "910671384069722112" %}}{{% tweet "903786057182957568" %}}{{% tweet "899635001247059969" %}}{{% tweet "898729425168080897" %}}{{% tweet "891144389715783680" %}}{{% tweet "883301626022375424" %}}{{% tweet "883246854695256064" %}}{{% tweet "877576023109390336" %}}{{% tweet "875594411584782337" %}}{{% tweet "871775262152810496" %}}{{% tweet "867408666852511744" %}}{{% tweet "857665638600507393" %}}{{% tweet "840181267542994944" %}}{{% tweet "839831849736232962" %}}{{% tweet "830023569887391744" %}}{{% tweet "829398997735313408" %}}{{% tweet "824264788456984576" %}}{{% tweet "822383911258890242" %}}{{% tweet "811666431452450816" %}}{{% tweet "811661275889549312" %}}{{% tweet "797041236867686400" %}}{{% tweet "797037016403820546" %}}{{% tweet "794278716859879424" %}}{{% tweet "831952966701678592" %}}{{% tweet "788751417746059264" %}}{{% tweet "693123105707986944" %}}{{% tweet "691762302492790788" %}}{{% tweet "687933344219312128" %}}{{% tweet "684411780412526592" %}}{{% tweet "665188011047563268" %}}{{% tweet "664040586001915904" %}}{{% tweet "639507420054749184" %}}{{% tweet "671673570259509248" %}}{{% tweet "667490462693912576" %}}{{% tweet "660278158663401473" %}}{{% tweet "641251456595685376" %}}{{% tweet "559734740488818688" %}}{{% tweet "559762891478667264" %}}{{% tweet "561514846291001344" %}}{{% tweet "559542705663905793" %}}{{% tweet "561056244782227456" %}}{{% tweet "664085841766195200" %}}{{% tweet "664431087683260416" %}}{{% tweet "667706456045694976" %}}{{% tweet "663937183791759360" %}}{{% tweet "663771499589861376" %}}{{% tweet "667433534756397057" %}}{{% tweet "640573716733169664" %}}{{% tweet "664407764001779712" %}}{{% tweet "630500659960254464" %}}{{% tweet "547497335412899840" %}}{{% tweet "610364467939913728" %}}</p>
11 
+<p>{{% tweet "941463119490150405" %}}{{% tweet "941040327816892416" %}}{{% tweet "940738021514547201" %}}{{% tweet "940337892030910467" %}}{{% tweet "938702392450617344" %}}{{% tweet "936241103585517568" %}}{{% tweet "920370392451178496" %}}{{% tweet "912971120198012929" %}}{{% tweet "907543915686793217" %}}{{% tweet "910671384069722112" %}}{{% tweet "903786057182957568" %}}{{% tweet "899635001247059969" %}}{{% tweet "898729425168080897" %}}{{% tweet "891144389715783680" %}}{{% tweet "883301626022375424" %}}{{% tweet "883246854695256064" %}}{{% tweet "877576023109390336" %}}{{% tweet "875594411584782337" %}}{{% tweet "871775262152810496" %}}{{% tweet "867408666852511744" %}}{{% tweet "857665638600507393" %}}{{% tweet "840181267542994944" %}}{{% tweet "839831849736232962" %}}{{% tweet "830023569887391744" %}}{{% tweet "829398997735313408" %}}{{% tweet "824264788456984576" %}}{{% tweet "822383911258890242" %}}{{% tweet "811666431452450816" %}}{{% tweet "811661275889549312" %}}{{% tweet "797041236867686400" %}}{{% tweet "797037016403820546" %}}{{% tweet "794278716859879424" %}}{{% tweet "831952966701678592" %}}{{% tweet "788751417746059264" %}}{{% tweet "693123105707986944" %}}{{% tweet "691762302492790788" %}}{{% tweet "687933344219312128" %}}{{% tweet "684411780412526592" %}}{{% tweet "665188011047563268" %}}{{% tweet "664040586001915904" %}}{{% tweet "639507420054749184" %}}{{% tweet "671673570259509248" %}}{{% tweet "667490462693912576" %}}{{% tweet "660278158663401473" %}}{{% tweet "641251456595685376" %}}{{% tweet "559734740488818688" %}}{{% tweet "559762891478667264" %}}{{% tweet "561514846291001344" %}}{{% tweet "559542705663905793" %}}{{% tweet "561056244782227456" %}}{{% tweet "664085841766195200" %}}{{% tweet "664431087683260416" %}}{{% tweet "667706456045694976" %}}{{% tweet "663937183791759360" %}}{{% tweet "663771499589861376" %}}{{% tweet "667433534756397057" %}}{{% tweet "640573716733169664" %}}{{% tweet "664407764001779712" %}}{{% tweet "630500659960254464" %}}{{% tweet "547497335412899840" %}}{{% tweet "610364467939913728" %}}</p>
site_src/content/tweets/index.rmd
History View file @ 887bd02
... ... 
@@ -11,6 +11,11 @@ weight: 50
11 11
12 12
13 13 
 ````{r echo=FALSE}
14 
+blogdown::shortcode('tweet', '941463119490150405')
15 
+blogdown::shortcode('tweet', '941040327816892416')
16 
+blogdown::shortcode('tweet', '940738021514547201')
17 
+blogdown::shortcode('tweet', '940337892030910467')
18 
+blogdown::shortcode('tweet', '938702392450617344')
14 19 
 blogdown::shortcode('tweet', '936241103585517568')
15 20 
 blogdown::shortcode('tweet', '920370392451178496')
16 21 
 blogdown::shortcode('tweet', '912971120198012929')