Browse code

update docs

guangchuang yu authored on 08/03/2017 07:27:32
Showing21 changed files

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@@ -53,11 +53,7 @@ mkdocs: mdfiles
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 mdfiles:
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 	cd mkdocs;\
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-	Rscript -e 'library(ypages); gendoc("src/index.md", "blue", "docs/index.md")';\
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-	Rscript -e 'library(ypages); gendoc("src/documentation.md", "blue", "docs/documentation.md")';\
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-	Rscript -e 'library(ypages); gendoc("src/featuredArticles.md", "blue", "docs/featuredArticles.md")';\
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-	Rscript -e 'library(ypages); gendoc("src/gallery.md", "blue", "docs/gallery.md")';\
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-	Rscript -e 'library(ypages); gendoc("src/faq.md", "blue", "docs/faq.md")';\
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+	Rscript -e 'source("render.R")';\
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 	cd docs;\
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 	ln -f -s ../mysoftware/* ./
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@@ -18,11 +18,11 @@ library("ypages")
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 <img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" />
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-`r badge_release("ggtree", "green")`
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+`r badge_bioc_release("ggtree", "green")`
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 `r badge_devel("ggtree", "green")`
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 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
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-`r badge_download("ggtree", "total", "blue")`
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-`r badge_download("ggtree", "month", "blue")`
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+`r badge_bioc_download("ggtree", "total", "blue")`
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+`r badge_bioc_download("ggtree", "month", "blue")`
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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)
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@@ -77,8 +77,8 @@ txtplot(d$year, d$cites)
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 ### Download stats
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 `r badge_download_bioc("ggtree")`
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-`r badge_download("ggtree", "total", "blue")`
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-`r badge_download("ggtree", "month", "blue")`
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+`r badge_bioc_download("ggtree", "total", "blue")`
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+`r badge_bioc_download("ggtree", "month", "blue")`
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 ```{r echo=F, comment=NA}
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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/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" />
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-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.10-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.9-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-22881/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1748/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.10-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.9-green.svg?style=flat)](https://github.com/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-12364/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-932/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--03--07-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--03--08-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) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
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@@ -53,7 +53,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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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) [![total](https://img.shields.io/badge/downloads-22881/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1748/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) [![total](https://img.shields.io/badge/downloads-12364/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-932/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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          ++-------------------+-------------------+--------------------+-------------------+-----------+
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          |                                                                                    *        |
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@@ -228,15 +228,14 @@
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 <!-- AddToAny BEGIN -->
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 <div class="a2a_kit a2a_kit_size_32 a2a_default_style">
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+
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 <a class="a2a_dd" href="//www.addtoany.com/share"></a>
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-<a class="a2a_button_facebook"></a>
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-<a class="a2a_button_twitter"></a>
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+<a class="a2a_button_facebook"></a> <a class="a2a_button_twitter"></a>
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 <a class="a2a_button_google_plus"></a>
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-<a class="a2a_button_pinterest"></a>
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-<a class="a2a_button_reddit"></a>
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-<a class="a2a_button_sina_weibo"></a>
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-<a class="a2a_button_wechat"></a>
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+<a class="a2a_button_pinterest"></a> <a class="a2a_button_reddit"></a>
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+<a class="a2a_button_sina_weibo"></a> <a class="a2a_button_wechat"></a>
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 <a class="a2a_button_douban"></a>
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 </div>
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 <script async src="//static.addtoany.com/menu/page.js"></script>
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@@ -247,88 +246,139 @@
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 <h2 id="vignettes"><i class="fa fa-book"></i> Vignettes</h2>
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 <ul>
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 <li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html">ggtree</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html">Tree Data Import</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">Tree Visualization</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html">Tree Annotation</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html">Tree Manipulation</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html">Advance Tree Annotation</a></li>
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-<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree utilities</a></li>
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+<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html">Tree Data
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+    Import</a></li>
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+<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html">Tree
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+    Visualization</a></li>
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+<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html">Tree
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+    Annotation</a></li>
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+<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html">Tree
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+    Manipulation</a></li>
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+<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html">Advance Tree
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+    Annotation</a></li>
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+<li><a href="https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html">ggtree
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+    utilities</a></li>
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 </ul>
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 <h2 id="blog-posts"><i class="fa fa-wordpress"></i> Blog posts</h2>
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 <h3 id="news-and-updates"><i class="fa fa-angle-double-right"></i> News and updates</h3>
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 <ul>
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-<li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1">ggtree in Bioconductor 3.1</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/12/news-of-ggtree">News of ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/">BioC 3.3: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC packages</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper published</a></li>
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+<li><a href="https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree">viewing and annotating phylogenetic tree with
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+    ggtree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1">ggtree in Bioconductor
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+    3.1</a></li>
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+<li><a href="https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages">BioC 3.1: NEWS of my BioC
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+    packages</a></li>
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+<li><a href="https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages">BioC 3.2: NEWS of my BioC
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+    packages</a></li>
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+<li><a href="https://guangchuangyu.github.io/2015/12/news-of-ggtree">News of
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+    ggtree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/">BioC 3.3: NEWS of my BioC
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+    packages</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages">BioC 3.4: NEWS of my BioC
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+    packages</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/08/ggtree-paper-published">ggtree paper
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+    published</a></li>
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 </ul>
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 <h3 id="data-manipulation"><i class="fa fa-angle-double-right"></i> Data manipulation</h3>
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 <ul>
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-<li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree format</a></li>
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-<li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using treeio</a></li>
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+<li><a href="https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree">subsetting data in
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+    ggtree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format">ggtree supports phylip tree
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+    format</a></li>
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+<li><a href="http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/">convert graphic object to tree object using
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+    treeio</a></li>
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 </ul>
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 <h3 id="tree-visualization"><i class="fa fa-angle-double-right"></i> Tree visualization</h3>
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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="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree
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+    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
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+    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
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+    ggtree</a>
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+    <i class="fa fa-arrow-left"></i> The Molecular Ecologist</li>
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 </ul>
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 <h3 id="tree-annotation"><i class="fa fa-angle-double-right"></i> Tree annotation</h3>
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 <ul>
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-<li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in ggtree</a></li>
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-<li><a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree">label edge number in
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+    ggtree</a></li>
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+<li><a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user
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+    data</a></li>
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 <li><a href="https://guangchuangyu.github.io/2015/08/subview">subview</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets">Annotate a phylogenetic tree with insets</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images">ggtree annotate phylogenetic tree with local images</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function">embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for ggtree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic tree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic tree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot output</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets">Annotate a phylogenetic tree with
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+    insets</a></li>
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+<li><a href="https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images">ggtree annotate phylogenetic tree with local
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+    images</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function">embed images in ggplot2 via subview and annotate a phylogenetic
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+    tree with images using inset
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+    function</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree">identify method for
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+    ggtree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/">facet_plot: a general solution to associate data with phylogenetic
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+    tree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/">align genomic features with phylogenetic
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+    tree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree
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+    panel</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/">add layer to specific panel of facet_plot
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+    output</a></li>
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 </ul>
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 <h3 id="tree-manipulation"><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://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree">flip and rotate branches in
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+    ggtree</a></li>
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 </ul>
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 <h3 id="application"><i class="fa fa-angle-double-right"></i> Application</h3>
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 <ul>
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-<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome data</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak data</a></li>
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-<li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of plotTree</a></li>
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-<li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/">ggtree for microbiome
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+    data</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/">ggtree for outbreak
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+    data</a></li>
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+<li><a href="http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/">ggtree version of
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+    plotTree</a></li>
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+<li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by
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+    ggtree</a></li>
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 </ul>
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 <h3 id="funny-stuff"><i class="fa fa-angle-double-right"></i> Funny stuff</h3>
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 <ul>
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-<li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>
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-<li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and comicR</a></li>
310
-<li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in R</a></li>
344
+<li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny
345
+    fonts</a></li>
346
+<li><a href="https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr">comic phylogenetic tree with ggtree and
347
+    comicR</a></li>
348
+<li><a href="https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r">use emoji font in
349
+    R</a></li>
311 350
 </ul>
312 351
 <h3 id="users-feedback"><i class="fa fa-angle-double-right"></i> User's feedback</h3>
313 352
 <ul>
314
-<li><a href="https://guangchuangyu.github.io/2016/02/tweets-of-ggtree">tweets of ggtree</a></li>
315
-<li>Join the group chat on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a></li>
353
+<li><a href="https://guangchuangyu.github.io/2016/02/tweets-of-ggtree">tweets of
354
+    ggtree</a></li>
355
+<li>Join the group chat on
356
+    <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a>
357
+    and
358
+    <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a></li>
316 359
 </ul>
317
-<p><i class="fa fa-hand-o-right"></i> Find out more on <a href="https://guangchuangyu.github.io/tags/ggtree/">https://guangchuangyu.github.io/tags/ggtree/</a>.</p>
360
+<p><i class="fa fa-hand-o-right"></i> Find out more on
361
+<a href="https://guangchuangyu.github.io/tags/ggtree/">https://guangchuangyu.github.io/tags/ggtree/</a>.</p>
318 362
 <h2 id="slides"><i class="fa fa-slideshare"></i> Slides</h2>
319 363
 <ul>
320
-<li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp; ggplot2</a></li>
321
-<li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic trees</a></li>
364
+<li><a href="https://guangchuangyu.github.io/presentation/2014-ggplot2/">Generating publication quality figures using R &amp;
365
+    ggplot2</a></li>
366
+<li><a href="https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/">ggtree for visualization and annotation of phylogenetic
367
+    trees</a></li>
322 368
 </ul>
323 369
 <h2 id="video"><i class="fa fa-youtube-play"></i> Video</h2>
324 370
 <ul>
325
-<li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade highlighting</a></li>
326
-<li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating clades</a></li>
327
-<li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade labeling</a></li>
371
+<li><a href="https://www.youtube.com/watch?v=KcF8Ec38mzI">interactive clade
372
+    highlighting</a></li>
373
+<li><a href="https://www.youtube.com/watch?v=lKNn4QlPO0E">interactive rotating
374
+    clades</a></li>
375
+<li><a href="https://www.youtube.com/watch?v=SmcceRD_jxg">interactive clade
376
+    labeling</a></li>
328 377
 </ul>
329 378
 <h2 id="workflow"><i class="fa fa-gift"></i> Workflow</h2>
330 379
 <ul>
331
-<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>
380
+<li><a href="https://rpubs.com/gutijosh9430/124817">recreate a tree from a publication (<strong>Bloom</strong> <em>et al</em>,
381
+    <strong><em>Science</em></strong> 2010)</a></li>
332 382
 </ul></div>
333 383
         </div>
334 384
 
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+
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241 240
 <script async src="//static.addtoany.com/menu/page.js"></script>
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@@ -245,11 +244,25 @@
245 244
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
246 245
 <h1 id="installation"><i class="fa fa-download"></i> Installation</h1>
247 246
 <h2 id="could-not-find-function"><i class="fa fa-angle-double-right"></i> Could not find function</h2>
248
-<p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this error</a>, please make sure you are using the latest R and <code>ggtree</code>.</p>
249
-<p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to <code>devel</code> branch.</p>
250
-<p>Sometimes I may write blog post to introduce new functions which is not available in <code>release</code> branch, you need to install the <code>devel</code> version of <code>ggtree</code> in order to use these new functions.</p>
251
-<p>You can download the <code>devel</code> version of <code>ggtree</code> from <a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and install it, or install the github version of <code>ggtree</code>.</p>
252
-<p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>, <code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the <code>could not find function</code> error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.</p>
247
+<p>If you got <a href="https://github.com/GuangchuangYu/ggtree/issues/12">this
248
+error</a>, please make
249
+sure you are using the latest R and <code>ggtree</code>.</p>
250
+<p>Packages in Bioconductor, like <code>ggtree</code>, have different release policy
251
+compare to CRAN. There are two branches, release and devel, in parallel.
252
+Release branch is more stable and only document improvement and bug
253
+fixes will commit to it. New functions will only commit to <code>devel</code>
254
+branch.</p>
255
+<p>Sometimes I may write blog post to introduce new functions which is not
256
+available in <code>release</code> branch, you need to install the <code>devel</code> version
257
+of <code>ggtree</code> in order to use these new functions.</p>
258
+<p>You can download the <code>devel</code> version of <code>ggtree</code> from
259
+<a href="http://bioconductor.org/packages/devel/bioc/html/ggtree.html">http://bioconductor.org/packages/devel/bioc/html/ggtree.html</a> and
260
+install it, or install the github version of <code>ggtree</code>.</p>
261
+<p>This also applied to other of my packages, including <code>GOSemSim</code>, <code>DOSE</code>,
262
+<code>clusterProfiler</code>, <code>ReactomePA</code> and <code>ChIPseeker</code>. If you got the
263
+<code>could not find function</code> error, upgrade your installation to latest
264
+release. If the error still exists after upgrading to latest release,
265
+you need to install the devel version.</p>
253 266
 <h1 id="text-label"><i class="fa fa-text-height"></i> Text &amp; Label</h1>
254 267
 <h2 id="tip-label-truncated"><i class="fa fa-angle-double-right"></i> Tip label truncated</h2>
255 268
 <p>ggplot2 can't auto adjust xlim based on added text.</p>
... ...
@@ -259,33 +272,37 @@ tree&lt;-read.tree(text=&quot;(Organism1.006G249400.1:0.03977,(Organism2.022118m
259 272
 ggtree(tree) + geom_tiplab()
260 273
 </code></pre>
261 274
 
262
-<p>This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.</p>
275
+<p>This is because the units are in two different spaces (data and pixel).
276
+Users can use xlim to allocate more space for tip label.</p>
263 277
 <pre><code class="r">ggtree(tree) + geom_tiplab() + xlim(0, 0.06)
264 278
 </code></pre>
265 279
 
266 280
 <h2 id="modify-tip-labels"><i class="fa fa-angle-double-right"></i> Modify (tip) labels</h2>
267
-<p>This could be easily done via the <code>%&lt;+%</code> operator to attach the
268
-modified version of the labels and than use <code>geom_tiplab</code> to display
269
-the modified version.</p>
270
-<pre><code>raxml_file &lt;- system.file(&quot;extdata/RAxML&quot;, &quot;RAxML_bipartitionsBranchLabels.H3&quot;, package=&quot;ggtree&quot;)
281
+<p>This could be easily done via the <code>%&lt;+%</code> operator to attach the modified
282
+version of the labels and than use <code>geom_tiplab</code> to display the modified
283
+version.</p>
284
+<pre><code>raxml_file &lt;- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree")
271 285
 raxml &lt;- read.raxml(raxml_file)
272 286
 
273 287
 lb = get.tree(raxml)$tip.label
274
-d = data.frame(label=lb, label2 = paste(&quot;AA&quot;, substring(lb, 1, 5)))
288
+d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5)))
275 289
 ggtree(raxml) %&lt;+% d + geom_tiplab(aes(label=label2))
276 290
 </code></pre>
277
-
278 291
 <p>see also
279 292
 <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ">1</a>
280 293
 and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
281 294
 <h2 id="formatting-tip-labels"><i class="fa fa-angle-double-right"></i> Formatting (tip) labels</h2>
282
-<p>If you want to format labels, you need to set <code>parse=TRUE</code> in <code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be parsed into expression and displayed as described in <code>?plotmath</code>.</p>
283
-<p>For example, the tiplabels contains two parts, species name and accession number and we want to display species name in <em>italic</em>, we can use command like this:</p>
284
-<pre><code>ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic(&quot;species name&quot;), &quot;accession number&quot;)', parse=T)
295
+<p>If you want to format labels, you need to set <code>parse=TRUE</code> in
296
+<code>geom_text</code>/<code>geom_tiplab</code> and the <code>label</code> should be string that can be
297
+parsed into expression and displayed as described in <code>?plotmath</code>.</p>
298
+<p>For example, the tiplabels contains two parts, species name and
299
+accession number and we want to display species name in <em>italic</em>, we can
300
+use command like this:</p>
301
+<pre><code>ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
285 302
 </code></pre>
286
-
287 303
 <h2 id="avoid-overlapping-text-labels"><i class="fa fa-angle-double-right"></i> Avoid overlapping text labels</h2>
288
-<p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a> package to repel overlapping text labels.</p>
304
+<p>User can use <a href="https://cran.r-project.org/web/packages/ggrepel/">ggrepel</a>
305
+package to repel overlapping text labels.</p>
289 306
 <p>For example:</p>
290 307
 <pre><code class="r">library(ggrepel)
291 308
 library(ggtree)
... ...
@@ -294,16 +311,28 @@ raxml &lt;- read.raxml(raxml_file)
294 311
 ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))
295 312
 </code></pre>
296 313
 
297
-<p>For details, please refer to <a href="https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html">ggrepel usage examples</a>.</p>
314
+<p>For details, please refer to <a href="https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html">ggrepel usage
315
+examples</a>.</p>
298 316
 <h2 id="bootstrap-values-from-newick-format"><i class="fa fa-angle-double-right"></i> bootstrap values from newick format</h2>
299
-<p>It's quite command to store <code>bootstrap</code> value as node label in <code>newick</code> format. Visualizing node label is easy using <code>geom_text2(aes(subset = !isTip, label=label))</code>.</p>
300
-<p>If you want to only display a subset of <code>bootstrap</code> (e.g. bootstrap &gt; 80), you can't simply using <code>geom_text2(subset= (label &gt; 80), label=label)</code> since <code>label</code> is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use <code>geom_text2(subset=(as.numeric(label) &gt; 80), label=label)</code>, it will also fail since <code>NAs</code> were introduced by coercion. We need to convert <code>NAs</code> to logical <code>FALSE</code>, this can be done by the following code:</p>
317
+<p>It's quite command to store <code>bootstrap</code> value as node label in <code>newick</code>
318
+format. Visualizing node label is easy using
319
+<code>geom_text2(aes(subset = !isTip, label=label))</code>.</p>
320
+<p>If you want to only display a subset of <code>bootstrap</code> (e.g. bootstrap &gt;
321
+80), you can't simply using
322
+<code>geom_text2(subset= (label &gt; 80), label=label)</code> since <code>label</code> is a
323
+character vector, which contains node label (bootstrap value) and tip
324
+label (taxa name). If we use
325
+<code>geom_text2(subset=(as.numeric(label) &gt; 80), label=label)</code>, it will also
326
+fail since <code>NAs</code> were introduced by coercion. We need to convert <code>NAs</code>
327
+to logical <code>FALSE</code>, this can be done by the following code:</p>
301 328
 <pre><code class="r">nwk &lt;- system.file(&quot;extdata/RAxML&quot;,&quot;RAxML_bipartitions.H3&quot;, package='ggtree')
302 329
 tr &lt;- read.tree(nwk)
303 330
 ggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) &amp; as.numeric(label) &gt; 80))
304 331
 </code></pre>
305 332
 
306
-<p>Another solution is converting the bootstrap value outside <code>ggtree</code> as I recommended in <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hiRBjGaAfI0/Y-2zDpvtAwAJ">google group</a>.</p>
333
+<p>Another solution is converting the bootstrap value outside <code>ggtree</code> as I
334
+recommended in <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hiRBjGaAfI0/Y-2zDpvtAwAJ">google
335
+group</a>.</p>
307 336
 <pre><code class="r">q &lt;- ggtree(tr)
308 337
 d &lt;- q$data
309 338
 d &lt;- d[!d$isTip,]
... ...
@@ -318,30 +347,40 @@ q + geom_text(data=d, aes(label=label))
318 347
 <pre><code class="r">ggtree(rtree(30)) + geom_point()
319 348
 </code></pre>
320 349
 
321
-<p>For example, we can add symbolic points to nodes with <code>geom_point()</code> directly.
322
-The magic here is we don't need to map <code>x</code> and <code>y</code> position of the points by providing <code>aes(x, y)</code> to <code>geom_point()</code> since it was already mapped by <code>ggtree</code> function and it serves as a global mapping for all layers.</p>
323
-<p>But what if we provide a <code>dataset</code> in a layer and the <code>dataset</code> doesn't contain column of <code>x</code> and/or <code>y</code>,
324
-the layer function also try to map <code>x</code> and <code>y</code> and also others if you map them in <code>ggtree</code> function.
325
-As these variable is not available in your <code>dataset</code>, you will get the following error:</p>
350
+<p>For example, we can add symbolic points to nodes with <code>geom_point()</code>
351
+directly. The magic here is we don't need to map <code>x</code> and <code>y</code> position of
352
+the points by providing <code>aes(x, y)</code> to <code>geom_point()</code> since it was
353
+already mapped by <code>ggtree</code> function and it serves as a global mapping
354
+for all layers.</p>
355
+<p>But what if we provide a <code>dataset</code> in a layer and the <code>dataset</code> doesn't
356
+contain column of <code>x</code> and/or <code>y</code>, the layer function also try to map <code>x</code>
357
+and <code>y</code> and also others if you map them in <code>ggtree</code> function. As these
358
+variable is not available in your <code>dataset</code>, you will get the following
359
+error:</p>
326 360
 <pre><code>Error in eval(expr, envir, enclos) : object 'x' not found
327 361
 </code></pre>
328
-
329
-<p>This can be fixed by using parameter <code>inherit.aes=FALSE</code> which will disable inheriting mapping from <code>ggtree</code> function.</p>
362
+<p>This can be fixed by using parameter <code>inherit.aes=FALSE</code> which will
363
+disable inheriting mapping from <code>ggtree</code> function.</p>
330 364
 <h2 id="use-in-aes"><i class="fa fa-angle-double-right"></i> use <code>$</code> in aes</h2>
331 365
 <p>NEVER DO THIS.</p>
332
-<p>see the explaination in the <a href="https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes">ggplot2 book 2ed</a>:</p>
366
+<p>see the explaination in the <a href="https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes">ggplot2 book
367
+2ed</a>:</p>
333 368
 <blockquote>
334
-<p>Never refer to a variable with <code>$</code> (e.g., <code>diamonds$carat</code>) in <code>aes()</code>. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.</p>
369
+<p>Never refer to a variable with <code>$</code> (e.g., <code>diamonds$carat</code>) in
370
+<code>aes()</code>. This breaks containment, so that the plot no longer contains
371
+everything it needs, and causes problems if ggplot2 changes the order
372
+of the rows, as it does when facetting.</p>
335 373
 </blockquote>
336 374
 <p>see also
337 375
 <a href="https://groups.google.com/forum/?utm_medium=email&amp;utm_source=footer#!msg/bioc-ggtree/hViM6vRZF94/MsZT8qRgBwAJ">1</a>
338 376
 and <a href="https://github.com/GuangchuangYu/ggtree/issues/106">2</a>.</p>
339 377
 <h1 id="annotation"><i class="fa fa-tree"></i> Annotation</h1>
340 378
 <h2 id="colouring-edges-by-user-data"><i class="fa fa-angle-double-right"></i> colouring edges by user data</h2>
341
-<p>see my blog post:
342
-<a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user data</a>
343
-and also my answer on <a href="https://github.com/GuangchuangYu/ggtree/issues/76">https://github.com/GuangchuangYu/ggtree/issues/76</a>
344
-and <a href="https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8">https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8</a>.</p></div>
379
+<p>see my blog post: <a href="http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/">Edge coloring with user
380
+data</a>
381
+and also my answer on
382
+<a href="https://github.com/GuangchuangYu/ggtree/issues/76">https://github.com/GuangchuangYu/ggtree/issues/76</a> and
383
+<a href="https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8">https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8</a>.</p></div>
345 384
         </div>
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+<!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->
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 <h2 id="2017"><i class="fa fa-calendar"></i> 2017</h2>
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-<p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging</a>. <strong><em>PNAS</em></strong>, 2017</p>
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-<p><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3">Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in <em>Bacteroides coprocola</em></a>. <strong><em>Microbiome</em></strong>, 2017, 5:15</p>
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+<p><a href="http://dx.doi.org/10.1073/pnas.1617959114">Phylogenetic analysis of the human antibody repertoire reveals
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+quantitative signatures of immune senescence and
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+aging</a>. <strong><em>PNAS</em></strong>, 2017</p>
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+<p><a href="https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0232-3">Gut metagenomes of type 2 diabetic patients have characteristic
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+single-nucleotide polymorphism distribution in <em>Bacteroides
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+coprocola</em></a>.
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+<strong><em>Microbiome</em></strong>, 2017, 5:15</p>
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 <h2 id="2016"><i class="fa fa-calendar"></i> 2016</h2>
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-<p><a href="http://aem.asm.org/content/82/22/6788.short">Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine</a>. <strong><em>Applied and Environmental Microbiology</em></strong>. 2016,82(22):6788-6798. </p></div>
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+<p><a href="http://aem.asm.org/content/82/22/6788.short">Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate
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+Transferases and Their Diversity in the Proximal Colon of
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+Swine</a>. <strong><em>Applied and
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+Environmental Microbiology</em></strong>. 2016,82(22):6788-6798.</p></div>
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248 249
 <h2 id="tweets"><i class="fa fa-twitter"></i> Tweets</h2>
249
-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">Adaptive radiation of <a href="https://twitter.com/hashtag/Darwin?src=hash">#Darwin</a>&#39;s finches showing <a href="https://twitter.com/hashtag/genotypic?src=hash">#genotypic</a> and <a href="https://twitter.com/hashtag/morphometric?src=hash">#morphometric</a> evolution. Good excuse to practice with <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a href="https://twitter.com/guangchuangyu">@guangchuangyu</a> <a href="https://t.co/JJZ3Yje58s">pic.twitter.com/JJZ3Yje58s</a></p>&mdash; Will Harvey (@_wharvey) <a href="https://twitter.com/_wharvey/status/831952966701678592">February 15, 2017</a></blockquote>
250
-
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-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">am quite liking <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="https://twitter.com/hashtag/ggplot?src=hash">#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">October 19, 2016</a></blockquote>
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-
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-<blockquote class="twitter-tweet" data-lang="en"><p lang="es" dir="ltr">Capital G, a reproducible logo produced by <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a href="https://twitter.com/hashtag/dataviz?src=hash">#dataviz</a> <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="https://twitter.com/hashtag/ggplot2?src=hash">#ggplot2</a> <a href="https://t.co/lJDcgfxAEh">pic.twitter.com/lJDcgfxAEh</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/786429360823644160">October 13, 2016</a></blockquote>
254
-
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-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">associate tree with different type of data by <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a href="https://t.co/6w755VWytZ">https://t.co/6w755VWytZ</a> <a href="https://t.co/K8WViEi13E">pic.twitter.com/K8WViEi13E</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/773359054924095488">September 7, 2016</a></blockquote>
256
-
257
-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">how about using emoji to label host species in phylogenetic tree? <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="https://twitter.com/hashtag/visualization?src=hash">#visualization</a> <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a href="https://twitter.com/hashtag/emojifont?src=hash">#emojifont</a> <a href="https://t.co/MRKQvNNAUh">pic.twitter.com/MRKQvNNAUh</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/708160510441566211">March 11, 2016</a></blockquote>
258
-
259
-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr"><a href="https://twitter.com/hashtag/phylomoji?src=hash">#phylomoji</a> with <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> <a href="https://t.co/yMUtm1jYF9">pic.twitter.com/yMUtm1jYF9</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/667337429704011777">November 19, 2015</a></blockquote>
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-
261
-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr">multiple sequence alignment with <a href="https://twitter.com/hashtag/phylogenetic?src=hash">#phylogenetic</a> tree via <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> pkg <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a>. <a href="http://t.co/6CY57dLdeb">pic.twitter.com/6CY57dLdeb</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/601676060254605312">May 22, 2015</a></blockquote>
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-
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-<blockquote class="twitter-tweet" data-lang="en"><p lang="en" dir="ltr"><a href="https://twitter.com/hashtag/comictree?src=hash">#comictree</a> via <a href="https://twitter.com/hashtag/ggtree?src=hash">#ggtree</a> and <a href="https://twitter.com/hashtag/comicR?src=hash">#comicR</a> in <a href="https://twitter.com/hashtag/rstats?src=hash">#rstats</a> <a href="http://t.co/zwCuOQ49bq">pic.twitter.com/zwCuOQ49bq</a></p>&mdash; Guangchuang Yu (@guangchuangyu) <a href="https://twitter.com/guangchuangyu/status/599078224576942080">May 15, 2015</a></blockquote>
250
+<blockquote class="twitter-tweet" data-lang="en">
251
+<p lang="en" dir="ltr">
252
+Adaptive radiation of
253
+<a href="https://twitter.com/hashtag/Darwin?src=hash">\#Darwin</a>'s
254
+finches showing
255
+<a href="https://twitter.com/hashtag/genotypic?src=hash">\#genotypic</a>
256
+and
257
+<a href="https://twitter.com/hashtag/morphometric?src=hash">\#morphometric</a>
258
+evolution. Good excuse to practice with
259
+<a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
260
+<a href="https://twitter.com/guangchuangyu">@guangchuangyu</a>
261
+<a href="https://t.co/JJZ3Yje58s">pic.twitter.com/JJZ3Yje58s</a>
262
+</p>
263
+— Will Harvey (@_wharvey)
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+<a href="https://twitter.com/_wharvey/status/831952966701678592">February
265
+15, 2017</a>
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+</blockquote>
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+
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+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="en" dir="ltr">
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+am quite liking
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+<a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
272
+<a href="https://twitter.com/hashtag/rstats?src=hash">\#rstats</a>
273
+<a href="https://twitter.com/hashtag/ggplot?src=hash">\#ggplot</a>
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+<a href="https://t.co/hvywS2z4ps">pic.twitter.com/hvywS2z4ps</a>
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+</p>
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+— Nicholas E Ilott (@IlottNick)
277
+<a href="https://twitter.com/IlottNick/status/788751417746059264">October
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+19, 2016</a>
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+</blockquote>
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+
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+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="es" dir="ltr">
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+Capital G, a reproducible logo produced by
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+<a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
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+<a href="https://twitter.com/hashtag/dataviz?src=hash">\#dataviz</a>
286
+<a href="https://twitter.com/hashtag/rstats?src=hash">\#rstats</a>
287
+<a href="https://twitter.com/hashtag/ggplot2?src=hash">\#ggplot2</a>
288
+<a href="https://t.co/lJDcgfxAEh">pic.twitter.com/lJDcgfxAEh</a>
289
+</p>
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+— Guangchuang Yu (@guangchuangyu)
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+<a href="https://twitter.com/guangchuangyu/status/786429360823644160">October
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+13, 2016</a>
293
+</blockquote>
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+
295
+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="en" dir="ltr">
297
+associate tree with different type of data by
298
+<a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
299
+<a href="https://t.co/6w755VWytZ">https://t.co/6w755VWytZ</a>
300
+<a href="https://t.co/K8WViEi13E">pic.twitter.com/K8WViEi13E</a>
301
+</p>
302
+— Guangchuang Yu (@guangchuangyu)
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+<a href="https://twitter.com/guangchuangyu/status/773359054924095488">September
304
+7, 2016</a>
305
+</blockquote>
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+
307
+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="en" dir="ltr">
309
+how about using emoji to label host species in phylogenetic tree?
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+<a href="https://twitter.com/hashtag/rstats?src=hash">\#rstats</a>
311
+<a href="https://twitter.com/hashtag/visualization?src=hash">\#visualization</a>
312
+<a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
313
+<a href="https://twitter.com/hashtag/emojifont?src=hash">\#emojifont</a>
314
+<a href="https://t.co/MRKQvNNAUh">pic.twitter.com/MRKQvNNAUh</a>
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+</p>
316
+— Guangchuang Yu (@guangchuangyu)
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+<a href="https://twitter.com/guangchuangyu/status/708160510441566211">March
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+11, 2016</a>
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+</blockquote>
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+
321
+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="en" dir="ltr">
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+<a href="https://twitter.com/hashtag/phylomoji?src=hash">\#phylomoji</a>
324
+with <a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
325
+<a href="https://t.co/yMUtm1jYF9">pic.twitter.com/yMUtm1jYF9</a>
326
+</p>
327
+— Guangchuang Yu (@guangchuangyu)
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+<a href="https://twitter.com/guangchuangyu/status/667337429704011777">November
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+19, 2015</a>
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+</blockquote>
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+
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+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="en" dir="ltr">
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+multiple sequence alignment with
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+<a href="https://twitter.com/hashtag/phylogenetic?src=hash">\#phylogenetic</a>
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+tree via
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+<a href="https://twitter.com/hashtag/rstats?src=hash">\#rstats</a> pkg
338
+<a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>.
339
+<a href="http://t.co/6CY57dLdeb">pic.twitter.com/6CY57dLdeb</a>
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+</p>
341
+— Guangchuang Yu (@guangchuangyu)
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+<a href="https://twitter.com/guangchuangyu/status/601676060254605312">May
343
+22, 2015</a>
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+</blockquote>
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+
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+<blockquote class="twitter-tweet" data-lang="en">
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+<p lang="en" dir="ltr">
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+<a href="https://twitter.com/hashtag/comictree?src=hash">\#comictree</a>
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+via <a href="https://twitter.com/hashtag/ggtree?src=hash">\#ggtree</a>
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+and <a href="https://twitter.com/hashtag/comicR?src=hash">\#comicR</a>
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+in <a href="https://twitter.com/hashtag/rstats?src=hash">\#rstats</a>
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+<a href="http://t.co/zwCuOQ49bq">pic.twitter.com/zwCuOQ49bq</a>
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+</p>
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+— Guangchuang Yu (@guangchuangyu)
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+<a href="https://twitter.com/guangchuangyu/status/599078224576942080">May
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+15, 2015</a>
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+</blockquote>
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+        <li class="main active"><a href="#ggtree-an-r-package-for-visualization-and-annotation-of-phylogenetic-trees-with-their-covariates-and-other-associated-data">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</a></li>
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-        <li class="main "><a href="#feedback"> Feedback</a></li>
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+            <li><a href="#feedback"> Feedback</a></li>
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 <img src="https://guangchuangyu.github.io/blog_images/biobabble.jpg" align="center" width="200"/>
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 <br>关注Y叔微信公众号biobabble
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+<h1 id="ggtree-an-r-package-for-visualization-and-annotation-of-phylogenetic-trees-with-their-covariates-and-other-associated-data">ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data</h1>
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+<a class="a2a_button_pinterest"></a> <a class="a2a_button_reddit"></a>
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+<a class="a2a_button_sina_weibo"></a> <a class="a2a_button_wechat"></a>
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245 229
 
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250 234
 <p><img src="https://raw.githubusercontent.com/jotsetung/BioC-stickers/master/ggtree/ggtree.png" height="128", align="right" /></p>
251 235
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
252 236
 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.10-blue.svg?style=flat" /></a>
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-<a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.9-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-22881/total-blue.svg?style=flat" /></a>
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-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1748/month-blue.svg?style=flat" /></a></p>
256
-<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.
257
-<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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+<a href="https://github.com/guangchuangyu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.9-blue.svg?style=flat" /></a>
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+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-12364/total-blue.svg?style=flat" /></a>
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+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-932/month-blue.svg?style=flat" /></a></p>
240
+<p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on
241
+grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>
242
+is designed for not only viewing phylogenetic tree but also displaying
243
+annotation data on the tree. <em>ggtree</em> is released within the
244
+<a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and
245
+the source code is hosted on
246
+<a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i>
247
+GitHub</a>.</p>
258 248
 <h2 id="authors"><i class="fa fa-user"></i> Authors</h2>
259
-<p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.</p>
249
+<p>Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The
250
+University of Hong Kong.</p>
260 251
 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>
261 252
 <p>Please cite the following article when using <code>ggtree</code>:</p>
262 253
 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="doi" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>
263 254
 <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-8-blue.svg?style=flat" /></a>
264 255
 <a href="https://www.altmetric.com/details/10533079"><img alt="Altmetric" src="https://img.shields.io/badge/Altmetric-352-blue.svg?style=flat" /></a></p>
265
-<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>
256
+<p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R
257
+package for visualization and annotation of phylogenetic trees with
258
+their covariates and other associated data. <strong><em>Methods in Ecology and
259
+Evolution</em></strong>. 2017, 8(1):28-36.</p>
266 260
 <h2 id="featured-articles"><i class="fa fa-pencil"></i> Featured Articles</h2>
267 261
 <p><img alt="" src="https://guangchuangyu.github.io/featured_img/ggtree/2015_peiyu_1-s2.0-S1567134815300721-gr1.jpg" /></p>
268
-<p><i class="fa fa-hand-o-right"></i> Find out more on <i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/ggtree/featuredArticles/">Featured Articles</a>.</p>
262
+<p><i class="fa fa-hand-o-right"></i> Find out more on
263
+<i class="fa fa-pencil"></i> <a href="https://guangchuangyu.github.io/ggtree/featuredArticles/">Featured
264
+Articles</a>.</p>
269 265
 <h2 id="installation"><i class="fa fa-download"></i> Installation</h2>
270
-<p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor page</a>:</p>
266
+<p>Install <code>ggtree</code> is easy, follow the guide on the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor
267
+page</a>:</p>
271 268
 <pre><code class="r">## try http:// if https:// URLs are not supported
272 269
 source(&quot;https://bioconductor.org/biocLite.R&quot;)
273 270
 ## biocLite(&quot;BiocUpgrade&quot;) ## you may need this
274 271
 biocLite(&quot;ggtree&quot;)
275 272
 </code></pre>
276 273
 
277
-<p>If you have problems when installing some of the dependent packages, please refer to the <a href="https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation">ggtree-installation</a> wiki page.</p>
274
+<p>If you have problems when installing some of the dependent packages,
275
+please refer to the
276
+<a href="https://github.com/GuangchuangYu/ggtree/wiki/ggtree-installation">ggtree-installation</a>
277
+wiki page.</p>
278 278
 <h2 id="overview"><i class="fa fa-cogs"></i> Overview</h2>
279 279
 <h4 id="getting-tree-into-r"><i class="fa fa-angle-double-right"></i> Getting tree into R</h4>
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 <ul>
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@@ -284,31 +284,41 @@ biocLite(&quot;ggtree&quot;)
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 </ul>
285 285
 <h4 id="tree-visualization-annotation"><i class="fa fa-angle-double-right"></i> Tree visualization &amp; annotation</h4>
286 286
 <ul>
287
-<li>parsing tree as a collection of nodes allows grammar of graphics to be supported</li>
287
+<li>parsing tree as a collection of nodes allows grammar of graphics to
288
+    be supported</li>
288 289
 <li><code>geom_tree</code>: extends <code>ggplot2</code> to support tree structure</li>
289 290
 <li>several layers and functions for tree annotation</li>
290 291
 <li>supports annotating phylogenetic trees with user's own data</li>
291 292
 </ul>
292 293
 <h4 id="tree-manipulation"><i class="fa fa-angle-double-right"></i> Tree manipulation</h4>
293 294
 <ul>
294
-<li>helper functions for tree manipulation, make it possible to explore the tree visually</li>
295
+<li>helper functions for tree manipulation, make it possible to explore
296
+    the tree visually</li>
295 297
 </ul>
296
-<p><i class="fa fa-hand-o-right"></i> Find out details and examples on <i class="fa fa-book"></i> <a href="https://guangchuangyu.github.io/ggtree/documentation/">Documentation</a>.</p>
298
+<p><i class="fa fa-hand-o-right"></i> Find out details and examples on
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+<i class="fa fa-book"></i>
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+<a href="https://guangchuangyu.github.io/ggtree/documentation/">Documentation</a>.</p>
297 301
 <h2 id="projects-that-depend-on-ggtree"><i class="fa fa-code-fork"></i> Projects that depend on <em>ggtree</em></h2>
298 302
 <h4 id="cran-packages"><i class="fa fa-angle-double-right"></i> CRAN packages</h4>
299 303
 <ul>
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-<li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle Phylogenetic Distance Matrices and Other Utilities</li>
304
+<li><a href="https://cran.r-project.org/package=harrietr">harrietr</a>: Wrangle
305
+    Phylogenetic Distance Matrices and Other Utilities</li>
301 306
 </ul>
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 <h4 id="bioconductor-packages"><i class="fa fa-angle-double-right"></i> Bioconductor packages</h4>
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 <ul>
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-<li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of lincRNAs and protein-coding genes</li>
305
-<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic partitioning based ILR transform for metagenomics data</li>
309
+<li><a href="https://www.bioconductor.org/packages/LINC">LINC</a>: co-expression of
310
+    lincRNAs and protein-coding genes</li>
311
+<li><a href="https://www.bioconductor.org/packages/philr">philr</a>: Phylogenetic
312
+    partitioning based ILR transform for metagenomics data</li>
306 313
 </ul>
307 314
 <h4 id="other-applications"><i class="fa fa-angle-double-right"></i> Other applications</h4>
308 315
 <ul>
309
-<li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>: Collection of scripts for metagenomics analysis</li>
310
-<li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>: Utilities for Creating and Validating Degenerate primers</li>
311
-<li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies created along a genome for patterns</li>
316
+<li><a href="https://bitbucket.org/biobakery/breadcrumbs">BreadCrumbs</a>:
317
+    Collection of scripts for metagenomics analysis</li>
318
+<li><a href="https://github.com/esnapd/DegeneratePrimerTools">DegeneratePrimerTools</a>:
319
+    Utilities for Creating and Validating Degenerate primers</li>
320
+<li><a href="https://github.com/olli0601/phyloscan">phyloscan</a>: scan phylogenies
321
+    created along a genome for patterns</li>
312 322
 </ul>
313 323
 <h2 id="feedback"><i class="fa fa-comments"></i> Feedback</h2>
314 324
 <ul class="fa-ul">
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@@ -317,6 +327,7 @@ biocLite(&quot;ggtree&quot;)
317 327
     <li><i class="fa-li fa fa-question"></i>  For user questions, please post to <i class="fa fa-google"></i> <a href="https://groups.google.com/forum/#!forum/bioc-ggtree">google group</a></li>
318 328
     <li><i class="fa-li fa fa-support"></i> We are also following every post tagged with <strong>ggtree</strong> on <a href="https://support.bioconductor.org">Bioconductor support site</a> and <a href="https://www.biostars.org">Biostars</a></li>
319 329
     <li><i class="fa-li fa fa-commenting"></i> Join the group chat on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a></li>
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+
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 </ul></div>
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         </div>
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@@ -2,27 +2,32 @@
2 2
     "docs": [
3 3
         {
4 4
             "location": "/", 
5
-            "text": "The \nggtree\n package extending the \nggplot2\n package. It based on grammar of graphics and takes all the good parts of \nggplot2\n.  \nggtree\n is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.\n\nggtree\n is released within the \nBioconductor\n project and the source code is hosted on \n GitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. \nMethods in Ecology and Evolution\n. 2017, 8(1):28-36.\n\n\n Featured Articles\n\n\n\n\n Find out more on \n \nFeatured Articles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor page\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages, please refer to the \nggtree-installation\n wiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore the tree visually\n\n\n\n\n Find out details and examples on \n \nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n CRAN packages\n\n\n\n\nharrietr\n: Wrangle Phylogenetic Distance Matrices and Other Utilities\n\n\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n: Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n: Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you have followed \nthe important guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and", 
5
+            "text": "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data\n\n\n\n\n\n\n\n\n\n\n \n\n\n\n\n \n\n\n \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nThe \nggtree\n package extending the \nggplot2\n package. It based on\ngrammar of graphics and takes all the good parts of \nggplot2\n. \nggtree\n\nis designed for not only viewing phylogenetic tree but also displaying\nannotation data on the tree. \nggtree\n is released within the\n\nBioconductor\n project and\nthe source code is hosted on\n\n\nGitHub\n.\n\n\n Authors\n\n\nGuangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The\nUniversity of Hong Kong.\n\n\n Citation\n\n\nPlease cite the following article when using \nggtree\n:\n\n\n\n\n\n\n\n\nG Yu\n, DK Smith, H Zhu, Y Guan, TTY Lam\n*\n. ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data. \nMethods in Ecology and\nEvolution\n. 2017, 8(1):28-36.\n\n\n Featured Articles\n\n\n\n\n Find out more on\n\n \nFeatured\nArticles\n.\n\n\n Installation\n\n\nInstall \nggtree\n is easy, follow the guide on the \nBioconductor\npage\n:\n\n\n## try http:// if https:// URLs are not supported\nsource(\nhttps://bioconductor.org/biocLite.R\n)\n## biocLite(\nBiocUpgrade\n) ## you may need this\nbiocLite(\nggtree\n)\n\n\n\n\nIf you have problems when installing some of the dependent packages,\nplease refer to the\n\nggtree-installation\n\nwiki page.\n\n\n Overview\n\n\n Getting tree into R\n\n\n\n\ntree parsers: bring evolution evidences to be used/analyzed in \nR\n\n\nmerge_tree\n: allows evolution evidences to be merged and compared\n\n\nfortify\n methods: convert tree objects into tidy data frame\n\n\n\n\n Tree visualization \n annotation\n\n\n\n\nparsing tree as a collection of nodes allows grammar of graphics to\n    be supported\n\n\ngeom_tree\n: extends \nggplot2\n to support tree structure\n\n\nseveral layers and functions for tree annotation\n\n\nsupports annotating phylogenetic trees with user's own data\n\n\n\n\n Tree manipulation\n\n\n\n\nhelper functions for tree manipulation, make it possible to explore\n    the tree visually\n\n\n\n\n Find out details and examples on\n\n\n\nDocumentation\n.\n\n\n Projects that depend on \nggtree\n\n\n CRAN packages\n\n\n\n\nharrietr\n: Wrangle\n    Phylogenetic Distance Matrices and Other Utilities\n\n\n\n\n Bioconductor packages\n\n\n\n\nLINC\n: co-expression of\n    lincRNAs and protein-coding genes\n\n\nphilr\n: Phylogenetic\n    partitioning based ILR transform for metagenomics data\n\n\n\n\n Other applications\n\n\n\n\nBreadCrumbs\n:\n    Collection of scripts for metagenomics analysis\n\n\nDegeneratePrimerTools\n:\n    Utilities for Creating and Validating Degenerate primers\n\n\nphyloscan\n: scan phylogenies\n    created along a genome for patterns\n\n\n\n\n Feedback\n\n\n\n    \n Please make sure you have followed \nthe important guide\n before posting any issue/question\n\n    \n For bugs or feature requests, please post to \n \ngithub issue\n\n    \n  For user questions, please post to \n \ngoogle group\n\n    \n We are also following every post tagged with \nggtree\n on \nBioconductor support site\n and \nBiostars\n\n    \n Join the group chat on \n and", 
6 6
             "title": "Home"
7 7
         }, 
8
+        {
9
+            "location": "/#ggtree-an-r-package-for-visualization-and-annotation-of-phylogenetic-trees-with-their-covariates-and-other-associated-data", 
10
+            "text": "The  ggtree  package extending the  ggplot2  package. It based on\ngrammar of graphics and takes all the good parts of  ggplot2 .  ggtree \nis designed for not only viewing phylogenetic tree but also displaying\nannotation data on the tree.  ggtree  is released within the Bioconductor  project and\nthe source code is hosted on \nGitHub .", 
11
+            "title": "ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data"
12
+        }, 
8 13
         {
9 14
             "location": "/#authors", 
10
-            "text": "Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.", 
15
+            "text": "Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The\nUniversity of Hong Kong.", 
11 16
             "title": " Authors"
12 17
         }, 
13 18
         {
14 19
             "location": "/#citation", 
15
-            "text": "Please cite the following article when using  ggtree :     G Yu , DK Smith, H Zhu, Y Guan, TTY Lam * . 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.", 
20
+            "text": "Please cite the following article when using  ggtree :     G Yu , DK Smith, H Zhu, Y Guan, TTY Lam * . ggtree: an R\npackage for visualization and annotation of phylogenetic trees with\ntheir covariates and other associated data.  Methods in Ecology and\nEvolution . 2017, 8(1):28-36.", 
16 21
             "title": " Citation"
17 22
         }, 
18 23
         {
19 24
             "location": "/#featured-articles", 
20
-            "text": "Find out more on    Featured Articles .", 
25
+            "text": "Find out more on   Featured\nArticles .", 
21 26
             "title": " Featured Articles"
22 27
         }, 
23 28
         {
24 29
             "location": "/#installation", 
25
-            "text": "Install  ggtree  is easy, follow the guide on the  Bioconductor page :  ## try http:// if https:// URLs are not supported\nsource( https://bioconductor.org/biocLite.R )\n## biocLite( BiocUpgrade ) ## you may need this\nbiocLite( ggtree )  If you have problems when installing some of the dependent packages, please refer to the  ggtree-installation  wiki page.", 
30
+            "text": "Install  ggtree  is easy, follow the guide on the  Bioconductor\npage :  ## try http:// if https:// URLs are not supported\nsource( https://bioconductor.org/biocLite.R )\n## biocLite( BiocUpgrade ) ## you may need this\nbiocLite( ggtree )  If you have problems when installing some of the dependent packages,\nplease refer to the ggtree-installation \nwiki page.", 
26 31
             "title": " Installation"
27 32
         }, 
28 33
         {
... ...
@@ -37,12 +42,12 @@
37 42
         }, 
38 43
         {
39 44
             "location": "/#tree-visualization-annotation", 
40
-            "text": "parsing tree as a collection of nodes allows grammar of graphics to be supported  geom_tree : extends  ggplot2  to support tree structure  several layers and functions for tree annotation  supports annotating phylogenetic trees with user's own data", 
45
+            "text": "parsing tree as a collection of nodes allows grammar of graphics to\n    be supported  geom_tree : extends  ggplot2  to support tree structure  several layers and functions for tree annotation  supports annotating phylogenetic trees with user's own data", 
41 46
             "title": " Tree visualization &amp; annotation"
42 47
         }, 
43 48
         {
44 49
             "location": "/#tree-manipulation", 
45
-            "text": "helper functions for tree manipulation, make it possible to explore the tree visually    Find out details and examples on    Documentation .", 
50
+            "text": "helper functions for tree manipulation, make it possible to explore\n    the tree visually    Find out details and examples on  Documentation .", 
46 51
             "title": " Tree manipulation"
47 52
         }, 
48 53
         {
... ...
@@ -52,17 +57,17 @@
52 57
         }, 
53 58
         {
54 59
             "location": "/#cran-packages", 
55
-            "text": "harrietr : Wrangle Phylogenetic Distance Matrices and Other Utilities", 
60
+            "text": "harrietr : Wrangle\n    Phylogenetic Distance Matrices and Other Utilities", 
56 61
             "title": " CRAN packages"
57 62
         }, 
58 63
         {
59 64
             "location": "/#bioconductor-packages", 
60
-            "text": "LINC : co-expression of lincRNAs and protein-coding genes  philr : Phylogenetic partitioning based ILR transform for metagenomics data", 
65
+            "text": "LINC : co-expression of\n    lincRNAs and protein-coding genes  philr : Phylogenetic\n    partitioning based ILR transform for metagenomics data", 
61 66
             "title": " Bioconductor packages"
62 67
         }, 
63 68
         {
64 69
             "location": "/#other-applications", 
65
-            "text": "BreadCrumbs : Collection of scripts for metagenomics analysis  DegeneratePrimerTools : Utilities for Creating and Validating Degenerate primers  phyloscan : scan phylogenies created along a genome for patterns", 
70
+            "text": "BreadCrumbs :\n    Collection of scripts for metagenomics analysis  DegeneratePrimerTools :\n    Utilities for Creating and Validating Degenerate primers  phyloscan : scan phylogenies\n    created along a genome for patterns", 
66 71
             "title": " Other applications"
67 72
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             "location": "/documentation/", 
75
-            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\nconvert graphic object to tree object using treeio\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\nPhylogenetic trees in R using ggtree\n \n The Molecular Ecologist\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nEdge coloring with user data\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\nalign genomic features with phylogenetic tree\n\n\nxlim_tree: set x axis limits for only Tree panel\n\n\nadd layer to specific panel of facet_plot output\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)", 
80
+            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data\n    Import\n\n\nTree\n    Visualization\n\n\nTree\n    Annotation\n\n\nTree\n    Manipulation\n\n\nAdvance Tree\n    Annotation\n\n\nggtree\n    utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with\n    ggtree\n\n\nggtree in Bioconductor\n    3.1\n\n\nBioC 3.1: NEWS of my BioC\n    packages\n\n\nBioC 3.2: NEWS of my BioC\n    packages\n\n\nNews of\n    ggtree\n\n\nBioC 3.3: NEWS of my BioC\n    packages\n\n\nBioC 3.4: NEWS of my BioC\n    packages\n\n\nggtree paper\n    published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in\n    ggtree\n\n\nggtree supports phylip tree\n    format\n\n\nconvert graphic object to tree object using\n    treeio\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree\n    view\n\n\nan example of drawing beast tree using\n    ggtree\n\n\nPhylogenetic trees in R using\n    ggtree\n\n    \n The Molecular Ecologist\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in\n    ggtree\n\n\nEdge coloring with user\n    data\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with\n    insets\n\n\nggtree annotate phylogenetic tree with local\n    images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic\n    tree with images using inset\n    function\n\n\nidentify method for\n    ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic\n    tree\n\n\nalign genomic features with phylogenetic\n    tree\n\n\nxlim_tree: set x axis limits for only Tree\n    panel\n\n\nadd layer to specific panel of facet_plot\n    output\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in\n    ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome\n    data\n\n\nggtree for outbreak\n    data\n\n\nggtree version of\n    plotTree\n\n\nreproducible logo generated by\n    ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny\n    fonts\n\n\ncomic phylogenetic tree with ggtree and\n    comicR\n\n\nuse emoji font in\n    R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of\n    ggtree\n\n\nJoin the group chat on\n    \n\n    and\n    \n\n\n\n\n Find out more on\n\nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n\n    ggplot2\n\n\nggtree for visualization and annotation of phylogenetic\n    trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade\n    highlighting\n\n\ninteractive rotating\n    clades\n\n\ninteractive clade\n    labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n,\n    \nScience\n 2010)", 
76 81
             "title": "Documentation"
77 82
         }, 
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         {
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             "location": "/documentation/#vignettes", 
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-            "text": "ggtree  Tree Data Import  Tree Visualization  Tree Annotation  Tree Manipulation  Advance Tree Annotation  ggtree utilities", 
85
+            "text": "ggtree  Tree Data\n    Import  Tree\n    Visualization  Tree\n    Annotation  Tree\n    Manipulation  Advance Tree\n    Annotation  ggtree\n    utilities", 
81 86
             "title": " Vignettes"
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         }, 
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         {
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@@ -87,62 +92,62 @@
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         }, 
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         {
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             "location": "/documentation/#news-and-updates", 
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-            "text": "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", 
95
+            "text": "viewing and annotating phylogenetic tree with\n    ggtree  ggtree in Bioconductor\n    3.1  BioC 3.1: NEWS of my BioC\n    packages  BioC 3.2: NEWS of my BioC\n    packages  News of\n    ggtree  BioC 3.3: NEWS of my BioC\n    packages  BioC 3.4: NEWS of my BioC\n    packages  ggtree paper\n    published", 
91 96
             "title": " News and updates"
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         }, 
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         {
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             "location": "/documentation/#data-manipulation", 
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-            "text": "subsetting data in ggtree  ggtree supports phylip tree format  convert graphic object to tree object using treeio", 
100
+            "text": "subsetting data in\n    ggtree  ggtree supports phylip tree\n    format  convert graphic object to tree object using\n    treeio", 
96 101
             "title": " Data manipulation"
97 102
         }, 
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         {
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             "location": "/documentation/#tree-visualization", 
100
-            "text": "ggtree - updating a tree view  an example of drawing beast tree using ggtree  Phylogenetic trees in R using ggtree    The Molecular Ecologist", 
105
+            "text": "ggtree - updating a tree\n    view  an example of drawing beast tree using\n    ggtree  Phylogenetic trees in R using\n    ggtree \n      The Molecular Ecologist", 
101 106
             "title": " Tree visualization"
102 107
         }, 
103 108
         {
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             "location": "/documentation/#tree-annotation", 
105
-            "text": "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  xlim_tree: set x axis limits for only Tree panel  add layer to specific panel of facet_plot output", 
110
+            "text": "label edge number in\n    ggtree  Edge coloring with user\n    data  subview  Annotate a phylogenetic tree with\n    insets  ggtree annotate phylogenetic tree with local\n    images  embed images in ggplot2 via subview and annotate a phylogenetic\n    tree with images using inset\n    function  identify method for\n    ggtree  facet_plot: a general solution to associate data with phylogenetic\n    tree  align genomic features with phylogenetic\n    tree  xlim_tree: set x axis limits for only Tree\n    panel  add layer to specific panel of facet_plot\n    output", 
106 111
             "title": " Tree annotation"
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         }, 
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         {
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             "location": "/documentation/#tree-manipulation", 
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-            "text": "flip and rotate branches in ggtree", 
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+            "text": "flip and rotate branches in\n    ggtree", 
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             "title": " Tree manipulation"
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         }, 
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         {
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             "location": "/documentation/#application", 
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-            "text": "ggtree for microbiome data  ggtree for outbreak data  ggtree version of plotTree  reproducible logo generated by ggtree", 
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+            "text": "ggtree for microbiome\n    data  ggtree for outbreak\n    data  ggtree version of\n    plotTree  reproducible logo generated by\n    ggtree", 
116 121
             "title": " Application"
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         }, 
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         {
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             "location": "/documentation/#funny-stuff", 
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-            "text": "ggtree with funny fonts  comic phylogenetic tree with ggtree and comicR  use emoji font in R", 
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+            "text": "ggtree with funny\n    fonts  comic phylogenetic tree with ggtree and\n    comicR  use emoji font in\n    R", 
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             "title": " Funny stuff"
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         }, 
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         {
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             "location": "/documentation/#users-feedback", 
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-            "text": "tweets of ggtree  Join the group chat on   and     Find out more on  https://guangchuangyu.github.io/tags/ggtree/ .", 
130
+            "text": "tweets of\n    ggtree  Join the group chat on\n     \n    and\n        Find out more on https://guangchuangyu.github.io/tags/ggtree/ .", 
126 131
             "title": " User's feedback"
127 132
         }, 
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         {
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             "location": "/documentation/#slides", 
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-            "text": "Generating publication quality figures using R   ggplot2  ggtree for visualization and annotation of phylogenetic trees", 
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+            "text": "Generating publication quality figures using R  \n    ggplot2  ggtree for visualization and annotation of phylogenetic\n    trees", 
131 136
             "title": " Slides"
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         }, 
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         {
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             "location": "/documentation/#video", 
135
-            "text": "interactive clade highlighting  interactive rotating clades  interactive clade labeling", 
140
+            "text": "interactive clade\n    highlighting  interactive rotating\n    clades  interactive clade\n    labeling", 
136 141
             "title": " Video"
137 142
         }, 
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         {
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             "location": "/documentation/#workflow", 
140
-            "text": "recreate a tree from a publication ( Bloom   et al ,  Science  2010)", 
145
+            "text": "recreate a tree from a publication ( Bloom   et al ,\n     Science  2010)", 
141 146
             "title": " Workflow"
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         }, 
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         {
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             "location": "/faq/", 
145
-            "text": "Installation\n\n\n Could not find function\n\n\nIf you got \nthis error\n, please make sure you are using the latest R and \nggtree\n.\n\n\nPackages in Bioconductor, like \nggtree\n, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to \ndevel\n branch.\n\n\nSometimes I may write blog post to introduce new functions which is not available in \nrelease\n branch, you need to install the \ndevel\n version of \nggtree\n in order to use these new functions.\n\n\nYou can download the \ndevel\n version of \nggtree\n from \nhttp://bioconductor.org/packages/devel/bioc/html/ggtree.html\n and install it, or install the github version of \nggtree\n.\n\n\nThis also applied to other of my packages, including \nGOSemSim\n, \nDOSE\n, \nclusterProfiler\n, \nReactomePA\n and \nChIPseeker\n. If you got the \ncould not find function\n error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you 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). Users 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\nmodified version of the labels and than use \ngeom_tiplab\n to display\nthe modified version.\n\n\nraxml_file \n- system.file(\nextdata/RAxML\n, \nRAxML_bipartitionsBranchLabels.H3\n, package=\nggtree\n)\nraxml \n- read.raxml(raxml_file)\n\nlb = get.tree(raxml)$tip.label\nd = data.frame(label=lb, label2 = paste(\nAA\n, substring(lb, 1, 5)))\nggtree(raxml) %\n+% d + geom_tiplab(aes(label=label2))\n\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 \ngeom_text\n/\ngeom_tiplab\n and the \nlabel\n should be string that can be parsed into expression and displayed as described in \n?plotmath\n.\n\n\nFor example, the tiplabels contains two parts, species name and accession number and we want to display species name in \nitalic\n, we can use command like this:\n\n\nggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic(\nspecies name\n), \naccession number\n)', parse=T)\n\n\n\n\n Avoid overlapping text labels\n\n\nUser can use \nggrepel\n package 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 examples\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 format. Visualizing node label is easy using \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 80), you can't simply using \ngeom_text2(subset= (label \n 80), label=label)\n since \nlabel\n is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use \ngeom_text2(subset=(as.numeric(label) \n 80), label=label)\n, it will also fail since \nNAs\n were introduced by coercion. We need to convert \nNAs\n to 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 recommended in \ngoogle group\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 directly.\nThe magic here is we don't need to map \nx\n and \ny\n position of the points by providing \naes(x, y)\n to \ngeom_point()\n since it was already mapped by \nggtree\n function and it serves as a global mapping for all layers.\n\n\nBut what if we provide a \ndataset\n in a layer and the \ndataset\n doesn't contain column of \nx\n and/or \ny\n,\nthe layer function also try to map \nx\n and \ny\n and also others if you map them in \nggtree\n function.\nAs these variable is not available in your \ndataset\n, you will get the following error:\n\n\nError in eval(expr, envir, enclos) : object 'x' not found\n\n\n\n\nThis can be fixed by using parameter \ninherit.aes=FALSE\n which will disable inheriting mapping from \nggtree\n function.\n\n\n use \n$\n in aes\n\n\nNEVER DO THIS.\n\n\nsee the explaination in the \nggplot2 book 2ed\n:\n\n\n\n\nNever refer to a variable with \n$\n (e.g., \ndiamonds$carat\n) in \naes()\n. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of 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:\n\nEdge coloring with user data\n\nand also my answer on \nhttps://github.com/GuangchuangYu/ggtree/issues/76\n\nand \nhttps://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8\n.", 
150
+            "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.", 
146 151
             "title": "FAQ"
147 152
         }, 
148 153
         {
... ...
@@ -152,7 +157,7 @@
152 157
         }, 
153 158
         {
154 159
             "location": "/faq/#could-not-find-function", 
155
-            "text": "If you got  this error , please make sure you are using the latest R and  ggtree .  Packages in Bioconductor, like  ggtree , have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to  devel  branch.  Sometimes I may write blog post to introduce new functions which is not available in  release  branch, you need to install the  devel  version of  ggtree  in order to use these new functions.  You can download the  devel  version of  ggtree  from  http://bioconductor.org/packages/devel/bioc/html/ggtree.html  and install it, or install the github version of  ggtree .  This also applied to other of my packages, including  GOSemSim ,  DOSE ,  clusterProfiler ,  ReactomePA  and  ChIPseeker . If you got the  could not find function  error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.", 
160
+            "text": "If you got  this\nerror , please make\nsure you are using the latest R and  ggtree .  Packages in Bioconductor, like  ggtree , 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  devel \nbranch.  Sometimes I may write blog post to introduce new functions which is not\navailable in  release  branch, you need to install the  devel  version\nof  ggtree  in order to use these new functions.  You can download the  devel  version of  ggtree  from http://bioconductor.org/packages/devel/bioc/html/ggtree.html  and\ninstall it, or install the github version of  ggtree .  This also applied to other of my packages, including  GOSemSim ,  DOSE , clusterProfiler ,  ReactomePA  and  ChIPseeker . If you got the could not find function  error, upgrade your installation to latest\nrelease. If the error still exists after upgrading to latest release,\nyou need to install the devel version.", 
156 161
             "title": " Could not find function"
157 162
         }, 
158 163
         {
... ...
@@ -162,27 +167,27 @@
162 167
         }, 
163 168
         {
164 169
             "location": "/faq/#tip-label-truncated", 
165
-            "text": "ggplot2 can't auto adjust xlim based on added text.  library(ggtree)\n## example tree from https://support.bioconductor.org/p/72398/\ntree -read.tree(text= (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); )\nggtree(tree) + geom_tiplab()  This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.  ggtree(tree) + geom_tiplab() + xlim(0, 0.06)", 
170
+            "text": "ggplot2 can't auto adjust xlim based on added text.  library(ggtree)\n## example tree from https://support.bioconductor.org/p/72398/\ntree -read.tree(text= (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); )\nggtree(tree) + geom_tiplab()  This is because the units are in two different spaces (data and pixel).\nUsers can use xlim to allocate more space for tip label.  ggtree(tree) + geom_tiplab() + xlim(0, 0.06)", 
166 171
             "title": " Tip label truncated"
167 172
         }, 
168 173
         {
169 174
             "location": "/faq/#modify-tip-labels", 
170
-            "text": "This could be easily done via the  % +%  operator to attach the\nmodified version of the labels and than use  geom_tiplab  to display\nthe modified version.  raxml_file  - system.file( extdata/RAxML ,  RAxML_bipartitionsBranchLabels.H3 , package= ggtree )\nraxml  - read.raxml(raxml_file)\n\nlb = get.tree(raxml)$tip.label\nd = data.frame(label=lb, label2 = paste( AA , substring(lb, 1, 5)))\nggtree(raxml) % +% d + geom_tiplab(aes(label=label2))  see also 1 \nand  2 .", 
175
+            "text": "This could be easily done via the  % +%  operator to attach the modified\nversion of the labels and than use  geom_tiplab  to display the modified\nversion.  raxml_file  - system.file(\"extdata/RAxML\", \"RAxML_bipartitionsBranchLabels.H3\", package=\"ggtree\")\nraxml  - read.raxml(raxml_file)\n\nlb = get.tree(raxml)$tip.label\nd = data.frame(label=lb, label2 = paste(\"AA\", substring(lb, 1, 5)))\nggtree(raxml) % +% d + geom_tiplab(aes(label=label2))  see also 1 \nand  2 .", 
171 176
             "title": " Modify (tip) labels"
172 177
         }, 
173 178
         {
174 179
             "location": "/faq/#formatting-tip-labels", 
175
-            "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 parsed into expression and displayed as described in  ?plotmath .  For example, the tiplabels contains two parts, species name and accession number and we want to display species name in  italic , we can use 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)", 
176 181
             "title": " Formatting (tip) labels"
177 182
         }, 
178 183
         {
179 184
             "location": "/faq/#avoid-overlapping-text-labels", 
180
-            "text": "User can use  ggrepel  package to repel overlapping text labels.  For example:  library(ggrepel)\nlibrary(ggtree)\nraxml_file  - system.file( extdata/RAxML ,  RAxML_bipartitionsBranchLabels.H3 , package= ggtree )\nraxml  - read.raxml(raxml_file)\nggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))  For details, please refer to  ggrepel usage examples .", 
185
+            "text": "User can use  ggrepel \npackage to repel overlapping text labels.  For example:  library(ggrepel)\nlibrary(ggtree)\nraxml_file  - system.file( extdata/RAxML ,  RAxML_bipartitionsBranchLabels.H3 , package= ggtree )\nraxml  - read.raxml(raxml_file)\nggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))  For details, please refer to  ggrepel usage\nexamples .", 
181 186
             "title": " Avoid overlapping text labels"
182 187
         }, 
183 188
         {
184 189
             "location": "/faq/#bootstrap-values-from-newick-format", 
185
-            "text": "It's quite command to store  bootstrap  value as node label in  newick  format. Visualizing node label is easy using  geom_text2(aes(subset = !isTip, label=label)) .  If you want to only display a subset of  bootstrap  (e.g. bootstrap   80), you can't simply using  geom_text2(subset= (label   80), label=label)  since  label  is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use  geom_text2(subset=(as.numeric(label)   80), label=label) , it will also fail since  NAs  were introduced by coercion. We need to convert  NAs  to logical  FALSE , this can be done by the following code:  nwk  - system.file( extdata/RAxML , RAxML_bipartitions.H3 , package='ggtree')\ntr  - read.tree(nwk)\nggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label))   as.numeric(label)   80))  Another solution is converting the bootstrap value outside  ggtree  as I recommended in  google group .  q  - ggtree(tr)\nd  - q$data\nd  - d[!d$isTip,]\nd$label  - as.numeric(d$label)\nd  - d[d$label   80,]\n\nq + geom_text(data=d, aes(label=label))", 
190
+            "text": "It's quite command to store  bootstrap  value as node label in  newick \nformat. Visualizing node label is easy using geom_text2(aes(subset = !isTip, label=label)) .  If you want to only display a subset of  bootstrap  (e.g. bootstrap  \n80), you can't simply using geom_text2(subset= (label   80), label=label)  since  label  is a\ncharacter vector, which contains node label (bootstrap value) and tip\nlabel (taxa name). If we use geom_text2(subset=(as.numeric(label)   80), label=label) , it will also\nfail since  NAs  were introduced by coercion. We need to convert  NAs \nto logical  FALSE , this can be done by the following code:  nwk  - system.file( extdata/RAxML , RAxML_bipartitions.H3 , package='ggtree')\ntr  - read.tree(nwk)\nggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label))   as.numeric(label)   80))  Another solution is converting the bootstrap value outside  ggtree  as I\nrecommended in  google\ngroup .  q  - ggtree(tr)\nd  - q$data\nd  - d[!d$isTip,]\nd$label  - as.numeric(d$label)\nd  - d[d$label   80,]\n\nq + geom_text(data=d, aes(label=label))", 
186 191
             "title": " bootstrap values from newick format"
187 192
         }, 
188 193
         {
... ...
@@ -192,12 +197,12 @@
192 197
         }, 
193 198
         {
194 199
             "location": "/faq/#inherit-aes", 
195
-            "text": "ggtree(rtree(30)) + geom_point()  For example, we can add symbolic points to nodes with  geom_point()  directly.\nThe magic here is we don't need to map  x  and  y  position of the points by providing  aes(x, y)  to  geom_point()  since it was already mapped by  ggtree  function and it serves as a global mapping for all layers.  But what if we provide a  dataset  in a layer and the  dataset  doesn't contain column of  x  and/or  y ,\nthe layer function also try to map  x  and  y  and also others if you map them in  ggtree  function.\nAs these variable is not available in your  dataset , you will get the following error:  Error in eval(expr, envir, enclos) : object 'x' not found  This can be fixed by using parameter  inherit.aes=FALSE  which will disable inheriting mapping from  ggtree  function.", 
200
+            "text": "ggtree(rtree(30)) + geom_point()  For example, we can add symbolic points to nodes with  geom_point() \ndirectly. The magic here is we don't need to map  x  and  y  position of\nthe points by providing  aes(x, y)  to  geom_point()  since it was\nalready mapped by  ggtree  function and it serves as a global mapping\nfor all layers.  But what if we provide a  dataset  in a layer and the  dataset  doesn't\ncontain column of  x  and/or  y , the layer function also try to map  x \nand  y  and also others if you map them in  ggtree  function. As these\nvariable is not available in your  dataset , you will get the following\nerror:  Error in eval(expr, envir, enclos) : object 'x' not found  This can be fixed by using parameter  inherit.aes=FALSE  which will\ndisable inheriting mapping from  ggtree  function.", 
196 201
             "title": " inherit aes"
197 202
         }, 
198 203
         {
199 204
             "location": "/faq/#use-in-aes", 
200
-            "text": "NEVER DO THIS.  see the explaination in the  ggplot2 book 2ed :   Never refer to a variable with  $  (e.g.,  diamonds$carat ) in  aes() . This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.   see also 1 \nand  2 .", 
205
+            "text": "NEVER DO THIS.  see the explaination in the  ggplot2 book\n2ed :   Never refer to a variable with  $  (e.g.,  diamonds$carat ) in aes() . 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.   see also 1 \nand  2 .", 
201 206
             "title": " use $ in aes"
202 207
         }, 
203 208
         {
... ...
@@ -207,27 +212,27 @@
207 212
         }, 
208 213
         {
209 214
             "location": "/faq/#colouring-edges-by-user-data", 
210
-            "text": "see my blog post: Edge coloring with user data \nand also my answer on  https://github.com/GuangchuangYu/ggtree/issues/76 \nand  https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8 .", 
215
+            "text": "see my blog post:  Edge coloring with user\ndata \nand also my answer on https://github.com/GuangchuangYu/ggtree/issues/76  and https://groups.google.com/forum/#!topic/bioc-ggtree/4GgivKqVjB8 .", 
211 216
             "title": " colouring edges by user data"
212 217
         }, 
213 218
         {
214 219
             "location": "/featuredArticles/", 
215
-            "text": "Let us know\n if you have published 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  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart191e3760ea02\",\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\":              7,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart191e3760ea02\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging\n. \nPNAS\n, 2017\n\n\nGut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in \nBacteroides coprocola\n. \nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine\n. \nApplied and Environmental 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\": \"chart561c721f7a23\",\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\":              7,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart561c721f7a23\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016,82(22):6788-6798.", 
216 221
             "title": "Featured Articles"
217 222
         }, 
218 223
         {
219 224
             "location": "/featuredArticles/#2017", 
220
-            "text": "Phylogenetic analysis of the human antibody repertoire reveals quantitative signatures of immune senescence and aging .  PNAS , 2017  Gut metagenomes of type 2 diabetic patients have characteristic single-nucleotide polymorphism distribution in  Bacteroides coprocola .  Microbiome , 2017, 5:15", 
225
+            "text": "Phylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging .  PNAS , 2017  Gut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in  Bacteroides\ncoprocola . Microbiome , 2017, 5:15", 
221 226
             "title": " 2017"
222 227
         }, 
223 228
         {
224 229
             "location": "/featuredArticles/#2016", 
225
-            "text": "Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate Transferases and Their Diversity in the Proximal Colon of Swine .  Applied and Environmental Microbiology . 2016,82(22):6788-6798.", 
230
+            "text": "Function and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine .  Applied and\nEnvironmental Microbiology . 2016,82(22):6788-6798.", 
226 231
             "title": " 2016"
227 232
         }, 
228 233
         {
229 234
             "location": "/gallery/", 
230
-            "text": "Journal Articles\n\n\n\n\nhttp://dx.doi.org/10.1186/s40168-017-0232-3\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1111/2041-210X.12628\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1128/AEM.02307-16\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\n\n\n Tweets\n\n\nAdaptive radiation of \n#Darwin\ns finches showing \n#genotypic\n and \n#morphometric\n evolution. Good excuse to practice with \n#ggtree\n \n@guangchuangyu\n \npic.twitter.com/JJZ3Yje58s\n Will Harvey (@_wharvey) \nFebruary 15, 2017\n\n\n\nam quite liking \n#ggtree\n \n#rstats\n \n#ggplot\n \npic.twitter.com/hvywS2z4ps\n Nicholas E Ilott (@IlottNick) \nOctober 19, 2016\n\n\n\nCapital G, a reproducible logo produced by \n#ggtree\n \n#dataviz\n \n#rstats\n \n#ggplot2\n \npic.twitter.com/lJDcgfxAEh\n Guangchuang Yu (@guangchuangyu) \nOctober 13, 2016\n\n\n\nassociate tree with different type of data by \n#ggtree\n \nhttps://t.co/6w755VWytZ\n \npic.twitter.com/K8WViEi13E\n Guangchuang Yu (@guangchuangyu) \nSeptember 7, 2016\n\n\n\nhow about using emoji to label host species in phylogenetic tree? \n#rstats\n \n#visualization\n \n#ggtree\n \n#emojifont\n \npic.twitter.com/MRKQvNNAUh\n Guangchuang Yu (@guangchuangyu) \nMarch 11, 2016\n\n\n\n#phylomoji\n with \n#ggtree\n \npic.twitter.com/yMUtm1jYF9\n Guangchuang Yu (@guangchuangyu) \nNovember 19, 2015\n\n\n\nmultiple sequence alignment with \n#phylogenetic\n tree via \n#rstats\n pkg \n#ggtree\n. \npic.twitter.com/6CY57dLdeb\n Guangchuang Yu (@guangchuangyu) \nMay 22, 2015\n\n\n\n#comictree\n via \n#ggtree\n and \n#comicR\n in \n#rstats\n \npic.twitter.com/zwCuOQ49bq\n Guangchuang Yu (@guangchuangyu) \nMay 15, 2015", 
235
+            "text": "Journal Articles\n\n\n\n\nhttp://dx.doi.org/10.1186/s40168-017-0232-3\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1111/2041-210X.12628\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1128/AEM.02307-16\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\n\n\n\n\n\n\nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\n\n\n Tweets\n\n\n\n\n\nAdaptive radiation of\n\n\\#Darwin\n's\nfinches showing\n\n\\#genotypic\n\nand\n\n\\#morphometric\n\nevolution. Good excuse to practice with\n\n\\#ggtree\n\n\n@guangchuangyu\n\n\npic.twitter.com/JJZ3Yje58s\n\n\n\n\u2014 Will Harvey (@_wharvey)\n\nFebruary\n15, 2017\n\n\n\n\n\n\n\n\nam quite liking\n\n\\#ggtree\n\n\n\\#rstats\n\n\n\\#ggplot\n\n\npic.twitter.com/hvywS2z4ps\n\n\n\n\u2014 Nicholas E Ilott (@IlottNick)\n\nOctober\n19, 2016\n\n\n\n\n\n\n\n\nCapital G, a reproducible logo produced by\n\n\\#ggtree\n\n\n\\#dataviz\n\n\n\\#rstats\n\n\n\\#ggplot2\n\n\npic.twitter.com/lJDcgfxAEh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nOctober\n13, 2016\n\n\n\n\n\n\n\n\nassociate tree with different type of data by\n\n\\#ggtree\n\n\nhttps://t.co/6w755VWytZ\n\n\npic.twitter.com/K8WViEi13E\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nSeptember\n7, 2016\n\n\n\n\n\n\n\n\nhow about using emoji to label host species in phylogenetic tree?\n\n\\#rstats\n\n\n\\#visualization\n\n\n\\#ggtree\n\n\n\\#emojifont\n\n\npic.twitter.com/MRKQvNNAUh\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMarch\n11, 2016\n\n\n\n\n\n\n\n\n\n\\#phylomoji\n\nwith \n\\#ggtree\n\n\npic.twitter.com/yMUtm1jYF9\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nNovember\n19, 2015\n\n\n\n\n\n\n\n\nmultiple sequence alignment with\n\n\\#phylogenetic\n\ntree via\n\n\\#rstats\n pkg\n\n\\#ggtree\n.\n\npic.twitter.com/6CY57dLdeb\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n22, 2015\n\n\n\n\n\n\n\n\n\n\\#comictree\n\nvia \n\\#ggtree\n\nand \n\\#comicR\n\nin \n\\#rstats\n\n\npic.twitter.com/zwCuOQ49bq\n\n\n\n\u2014 Guangchuang Yu (@guangchuangyu)\n\nMay\n15, 2015", 
231 236
             "title": "Gallery"
232 237
         }, 
233 238
         {
... ...
@@ -237,7 +242,7 @@
237 242
         }, 
238 243
         {
239 244
             "location": "/gallery/#tweets", 
240
-            "text": "Adaptive radiation of  #Darwin s finches showing  #genotypic  and  #morphometric  evolution. Good excuse to practice with  #ggtree   @guangchuangyu   pic.twitter.com/JJZ3Yje58s  Will Harvey (@_wharvey)  February 15, 2017  am quite liking  #ggtree   #rstats   #ggplot   pic.twitter.com/hvywS2z4ps  Nicholas E Ilott (@IlottNick)  October 19, 2016  Capital G, a reproducible logo produced by  #ggtree   #dataviz   #rstats   #ggplot2   pic.twitter.com/lJDcgfxAEh  Guangchuang Yu (@guangchuangyu)  October 13, 2016  associate tree with different type of data by  #ggtree   https://t.co/6w755VWytZ   pic.twitter.com/K8WViEi13E  Guangchuang Yu (@guangchuangyu)  September 7, 2016  how about using emoji to label host species in phylogenetic tree?  #rstats   #visualization   #ggtree   #emojifont   pic.twitter.com/MRKQvNNAUh  Guangchuang Yu (@guangchuangyu)  March 11, 2016  #phylomoji  with  #ggtree   pic.twitter.com/yMUtm1jYF9  Guangchuang Yu (@guangchuangyu)  November 19, 2015  multiple sequence alignment with  #phylogenetic  tree via  #rstats  pkg  #ggtree .  pic.twitter.com/6CY57dLdeb  Guangchuang Yu (@guangchuangyu)  May 22, 2015  #comictree  via  #ggtree  and  #comicR  in  #rstats   pic.twitter.com/zwCuOQ49bq  Guangchuang Yu (@guangchuangyu)  May 15, 2015", 
245
+            "text": "Adaptive radiation of \\#Darwin 's\nfinches showing \\#genotypic \nand \\#morphometric \nevolution. Good excuse to practice with \\#ggtree  @guangchuangyu  pic.twitter.com/JJZ3Yje58s  \n\u2014 Will Harvey (@_wharvey) February\n15, 2017    \nam quite liking \\#ggtree  \\#rstats  \\#ggplot  pic.twitter.com/hvywS2z4ps  \n\u2014 Nicholas E Ilott (@IlottNick) October\n19, 2016    \nCapital G, a reproducible logo produced by \\#ggtree  \\#dataviz  \\#rstats  \\#ggplot2  pic.twitter.com/lJDcgfxAEh  \n\u2014 Guangchuang Yu (@guangchuangyu) October\n13, 2016    \nassociate tree with different type of data by \\#ggtree  https://t.co/6w755VWytZ  pic.twitter.com/K8WViEi13E  \n\u2014 Guangchuang Yu (@guangchuangyu) September\n7, 2016    \nhow about using emoji to label host species in phylogenetic tree? \\#rstats  \\#visualization  \\#ggtree  \\#emojifont  pic.twitter.com/MRKQvNNAUh  \n\u2014 Guangchuang Yu (@guangchuangyu) March\n11, 2016     \\#phylomoji \nwith  \\#ggtree  pic.twitter.com/yMUtm1jYF9  \n\u2014 Guangchuang Yu (@guangchuangyu) November\n19, 2015    \nmultiple sequence alignment with \\#phylogenetic \ntree via \\#rstats  pkg \\#ggtree . pic.twitter.com/6CY57dLdeb  \n\u2014 Guangchuang Yu (@guangchuangyu) May\n22, 2015     \\#comictree \nvia  \\#ggtree \nand  \\#comicR \nin  \\#rstats  pic.twitter.com/zwCuOQ49bq  \n\u2014 Guangchuang Yu (@guangchuangyu) May\n15, 2015", 
241 246
             "title": " Tweets"
242 247
         }, 
243 248
         {
... ...
@@ -4,7 +4,7 @@
4 4
     
5 5
     <url>
6 6
      <loc>https://guangchuangyu.github.io/ggtree/</loc>
7
-     <lastmod>2017-03-07</lastmod>
7
+     <lastmod>2017-03-08</lastmod>
8 8
      <changefreq>daily</changefreq>
9 9
     </url>
10 10
     
... ...
@@ -12,7 +12,7 @@
12 12
     
13 13
     <url>
14 14
      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>
15
-     <lastmod>2017-03-07</lastmod>
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16 16
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     </url>
18 18
     
... ...
@@ -20,7 +20,7 @@
20 20
     
21 21
     <url>
22 22
      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>
23
-     <lastmod>2017-03-07</lastmod>
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24 24
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25 25
     </url>
26 26
     
... ...
@@ -28,7 +28,7 @@
28 28
     
29 29
     <url>
30 30
      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>
31
-     <lastmod>2017-03-07</lastmod>
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+     <lastmod>2017-03-08</lastmod>
32 32
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33 33
     </url>
34 34
     
... ...
@@ -36,7 +36,7 @@
36 36
     
37 37
     <url>
38 38
      <loc>https://guangchuangyu.github.io/ggtree/gallery/</loc>
39
-     <lastmod>2017-03-07</lastmod>
39
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40 40
      <changefreq>daily</changefreq>
41 41
     </url>
42 42
     
... ...
@@ -45,55 +45,55 @@
45 45
         
46 46
     <url>
47 47
      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>
48
-     <lastmod>2017-03-07</lastmod>
48
+     <lastmod>2017-03-08</lastmod>
49 49
      <changefreq>daily</changefreq>
50 50
     </url>
51 51
         
52 52
     <url>
53 53
      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>
54
-     <lastmod>2017-03-07</lastmod>
54
+     <lastmod>2017-03-08</lastmod>
55 55
      <changefreq>daily</changefreq>
56 56
     </url>
57 57
         
58 58
     <url>
59 59
      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>
60
-     <lastmod>2017-03-07</lastmod>
60
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61 61
      <changefreq>daily</changefreq>
62 62
     </url>
63 63
         
64 64
     <url>
65 65
      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>
66
-     <lastmod>2017-03-07</lastmod>
66
+     <lastmod>2017-03-08</lastmod>
67 67
      <changefreq>daily</changefreq>
68 68
     </url>
69 69
         
70 70
     <url>
71 71
      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>
72
-     <lastmod>2017-03-07</lastmod>
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73 73
      <changefreq>daily</changefreq>
74 74
     </url>
75 75
         
76 76
     <url>
77 77
      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>
78
-     <lastmod>2017-03-07</lastmod>
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+     <lastmod>2017-03-08</lastmod>
79 79
      <changefreq>daily</changefreq>
80 80
     </url>
81 81
         
82 82
     <url>
83 83
      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>
84
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85 85
      <changefreq>daily</changefreq>
86 86
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87 87
         
88 88
     <url>
89 89
      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>
90
-     <lastmod>2017-03-07</lastmod>
90
+     <lastmod>2017-03-08</lastmod>
91 91
      <changefreq>daily</changefreq>
92 92
     </url>
93 93
         
94 94
     <url>
95 95
      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>
96
-     <lastmod>2017-03-07</lastmod>
96
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97 97
      <changefreq>daily</changefreq>
98 98
     </url>
99 99
         
... ...
@@ -1,107 +1,166 @@
1
+---
2
+html_preview: False
3
+output:
4
+  md_document:
5
+    variant: markdown
6
+---
7
+
1 8
 <!-- AddToAny BEGIN -->
2 9
 <div class="a2a_kit a2a_kit_size_32 a2a_default_style">
10
+
3 11
 <a class="a2a_dd" href="//www.addtoany.com/share"></a>
4
-<a class="a2a_button_facebook"></a>
5
-<a class="a2a_button_twitter"></a>
12
+<a class="a2a_button_facebook"></a> <a class="a2a_button_twitter"></a>
6 13
 <a class="a2a_button_google_plus"></a>
7
-<a class="a2a_button_pinterest"></a>
8
-<a class="a2a_button_reddit"></a>
9
-<a class="a2a_button_sina_weibo"></a>
10
-<a class="a2a_button_wechat"></a>
14
+<a class="a2a_button_pinterest"></a> <a class="a2a_button_reddit"></a>
15
+<a class="a2a_button_sina_weibo"></a> <a class="a2a_button_wechat"></a>
11 16
 <a class="a2a_button_douban"></a>
17
+
12 18
 </div>
19
+
13 20
 <script async src="//static.addtoany.com/menu/page.js"></script>
14 21
 <!-- AddToAny END -->
15
-
16 22
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
17 23
 
18
-## <i class="fa fa-book"></i> Vignettes
19
-
20
-+ [ggtree](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html)
21
-+ [Tree Data Import](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html)
22
-+ [Tree Visualization](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html)
23
-+ [Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html)
24
-+ [Tree Manipulation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html)
25
-+ [Advance Tree Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html)
26
-+ [ggtree utilities](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html)
27
-
28
-
29
-## <i class="fa fa-wordpress"></i> Blog posts
24
+<i class="fa fa-book"></i> Vignettes
25
+------------------------------------
26
+
27
+-   [ggtree](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtree.html)
28
+-   [Tree Data
29
+    Import](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeImport.html)
30
+-   [Tree
31
+    Visualization](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html)
32
+-   [Tree
33
+    Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeAnnotation.html)
34
+-   [Tree
35
+    Manipulation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeManipulation.html)
36
+-   [Advance Tree
37
+    Annotation](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/advanceTreeAnnotation.html)
38
+-   [ggtree
39
+    utilities](https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/ggtreeUtilities.html)
40
+
41
+<i class="fa fa-wordpress"></i> Blog posts
42
+------------------------------------------
30 43
 
31 44
 ### <i class="fa fa-angle-double-right"></i> News and updates
32 45
 
33
-+ [viewing and annotating phylogenetic tree with ggtree](https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree)
34
-+ [ggtree in Bioconductor 3.1](https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1)
35
-+ [BioC 3.1: NEWS of my BioC packages](https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages)
36
-+ [BioC 3.2: NEWS of my BioC packages](https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages)
37
-+ [News of ggtree](https://guangchuangyu.github.io/2015/12/news-of-ggtree)
38
-+ [BioC 3.3: NEWS of my BioC packages](https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/)
39
-+ [BioC 3.4: NEWS of my BioC packages](https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages)
40
-+ [ggtree paper published](https://guangchuangyu.github.io/2016/08/ggtree-paper-published)
46
+-   [viewing and annotating phylogenetic tree with
47
+    ggtree](https://guangchuangyu.github.io/2014/12/viewing-and-annotating-phylogenetic-tree-with-ggtree)
48
+-   [ggtree in Bioconductor
49
+    3.1](https://guangchuangyu.github.io/2015/01/ggtree-in-bioconductor-3.1)
50
+-   [BioC 3.1: NEWS of my BioC
51
+    packages](https://guangchuangyu.github.io/2015/04/bioc-31-news-of-my-bioc-packages)
52
+-   [BioC 3.2: NEWS of my BioC
53
+    packages](https://guangchuangyu.github.io/2015/10/bioc-32-news-of-my-bioc-packages)
54
+-   [News of
55
+    ggtree](https://guangchuangyu.github.io/2015/12/news-of-ggtree)
56
+-   [BioC 3.3: NEWS of my BioC
57
+    packages](https://guangchuangyu.github.io/2016/05/bioc-33-news-of-my-bioc-packages/)
58
+-   [BioC 3.4: NEWS of my BioC
59
+    packages](https://guangchuangyu.github.io/2016/10/bioc-34-news-of-my-bioc-packages)
60
+-   [ggtree paper
61
+    published](https://guangchuangyu.github.io/2016/08/ggtree-paper-published)
41 62
 
42 63
 ### <i class="fa fa-angle-double-right"></i> Data manipulation
43 64
 
44
-+ [subsetting data in ggtree](https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree)
45
-+ [ggtree supports phylip tree format](https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format)
46
-+ [convert graphic object to tree object using treeio](http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/)
65
+-   [subsetting data in
66
+    ggtree](https://guangchuangyu.github.io/2015/09/subsetting-data-in-ggtree)
67
+-   [ggtree supports phylip tree
68
+    format](https://guangchuangyu.github.io/2016/01/ggtree-supports-phylip-tree-format)
69
+-   [convert graphic object to tree object using
70
+    treeio](http://guangchuangyu.github.io/2017/01/convert-graphic-object-to-tree-object-using-treeio/)
47 71
 
48 72
 ### <i class="fa fa-angle-double-right"></i> Tree visualization
49 73
 
50
-+ [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)
51
-+ [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)
52
-+ [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
74
+-   [ggtree - updating a tree
75
+    view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)
76
+-   [an example of drawing beast tree using
77
+    ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)
78
+-   [Phylogenetic trees in R using
79
+    ggtree](http://www.molecularecologist.com/2017/02/phylogenetic-trees-in-r-using-ggtree/)
80
+    <i class="fa fa-arrow-left"></i> The Molecular Ecologist
53 81
 
54 82
 ### <i class="fa fa-angle-double-right"></i> Tree annotation
55 83
 
56
-+ [label edge number in ggtree](https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree)
57
-+ [Edge coloring with user data](http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/)
58
-+ [subview](https://guangchuangyu.github.io/2015/08/subview)
59
-+ [Annotate a phylogenetic tree with insets](https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets)
60
-+ [ggtree annotate phylogenetic tree with local images](https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images)
61
-+ [embed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function](https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function)
62
-+ [identify method for ggtree](https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree)
63
-+ [facet_plot: a general solution to associate data with phylogenetic tree](https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/)
64
-+ [align genomic features with phylogenetic tree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/)
65
-+ [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)
66
-+ [add layer to specific panel of facet_plot output](https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/)
67
-
84
+-   [label edge number in
85
+    ggtree](https://guangchuangyu.github.io/2016/01/label-edge-number-in-ggtree)
86
+-   [Edge coloring with user
87
+    data](http://guangchuangyu.github.io/2016/12/edge-coloring-with-user-data/)
88
+-   [subview](https://guangchuangyu.github.io/2015/08/subview)
89
+-   [Annotate a phylogenetic tree with
90
+    insets](https://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets)
91
+-   [ggtree annotate phylogenetic tree with local
92
+    images](https://guangchuangyu.github.io/2015/08/ggtree-annotate-phylogenetic-tree-with-local-images)
93
+-   [embed images in ggplot2 via subview and annotate a phylogenetic
94
+    tree with images using inset
95
+    function](https://guangchuangyu.github.io/2016/03/embed-images-in-ggplot2-via-subview-and-annotate-a-phylogenetic-tree-with-images-using-inset-function)
96
+-   [identify method for
97
+    ggtree](https://guangchuangyu.github.io/2016/06/identify-method-for-ggtree)
98
+-   [facet\_plot: a general solution to associate data with phylogenetic
99
+    tree](https://guangchuangyu.github.io/2016/10/facet_plot-a-general-solution-to-associate-data-with-phylogenetic-tree/)
100
+-   [align genomic features with phylogenetic
101
+    tree](https://guangchuangyu.github.io/2016/11/align-genomic-features-with-phylogenetic-tree/)
102
+-   [xlim\_tree: set x axis limits for only Tree
103
+    panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)
104
+-   [add layer to specific panel of facet\_plot
105
+    output](https://guangchuangyu.github.io/2016/12/add-layer-to-specific-panel-of-facet_plot-output/)
68 106
 
69 107
 ### <i class="fa fa-angle-double-right"></i> Tree manipulation
70 108
 
71
-+ [flip and rotate branches in ggtree](https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree)
109
+-   [flip and rotate branches in
110
+    ggtree](https://guangchuangyu.github.io/2015/07/flip-and-rotate-branches-in-ggtree)
72 111
 
73 112
 ### <i class="fa fa-angle-double-right"></i> Application
74 113
 
75
-+ [ggtree for microbiome data](https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/)
76
-+ [ggtree for outbreak data](https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/)
77
-+ [ggtree version of plotTree](http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/)
78
-+ [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)
79
-
114
+-   [ggtree for microbiome
115
+    data](https://guangchuangyu.github.io/2016/09/ggtree-for-microbiome-data/)
116
+-   [ggtree for outbreak
117
+    data](https://guangchuangyu.github.io/2016/09/ggtree-for-outbreak-data/)
118
+-   [ggtree version of
119
+    plotTree](http://guangchuangyu.github.io/2016/12/ggtree-version-of-plottree/)
120
+-   [reproducible logo generated by
121
+    ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)
80 122
 
81 123
 ### <i class="fa fa-angle-double-right"></i> Funny stuff
82 124
 
83
-+ [ggtree with funny fonts](https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts)
84
-+ [comic phylogenetic tree with ggtree and comicR](https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr)
85
-+ [use emoji font in R](https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r)
125
+-   [ggtree with funny
126
+    fonts](https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts)
127
+-   [comic phylogenetic tree with ggtree and
128
+    comicR](https://guangchuangyu.github.io/2015/09/comic-phylogenetic-tree-with-ggtree-and-comicr)
129
+-   [use emoji font in
130
+    R](https://guangchuangyu.github.io/2015/12/use-emoji-font-in-r)
86 131
 
87 132
 ### <i class="fa fa-angle-double-right"></i> User's feedback
88 133
 
89
-+ [tweets of ggtree](https://guangchuangyu.github.io/2016/02/tweets-of-ggtree)
90
-+ Join the group chat on <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a> and <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a>
134
+-   [tweets of
135
+    ggtree](https://guangchuangyu.github.io/2016/02/tweets-of-ggtree)
136
+-   Join the group chat on
137
+    <a href="https://twitter.com/hashtag/ggtree"><i class="fa fa-twitter fa-lg"></i></a>
138
+    and
139
+    <a href="http://huati.weibo.com/k/ggtree"><i class="fa fa-weibo fa-lg"></i></a>
91 140
 
92
-<i class="fa fa-hand-o-right"></i> Find out more on <https://guangchuangyu.github.io/tags/ggtree/>.
141
+<i class="fa fa-hand-o-right"></i> Find out more on
142
+<https://guangchuangyu.github.io/tags/ggtree/>.
93 143
 
94
-## <i class="fa fa-slideshare"></i> Slides
144
+<i class="fa fa-slideshare"></i> Slides
145
+---------------------------------------
95 146
 
96
-+ [Generating publication quality figures using R & ggplot2](https://guangchuangyu.github.io/presentation/2014-ggplot2/)
97
-+ [ggtree for visualization and annotation of phylogenetic trees](https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/)
147
+-   [Generating publication quality figures using R &
148
+    ggplot2](https://guangchuangyu.github.io/presentation/2014-ggplot2/)
149
+-   [ggtree for visualization and annotation of phylogenetic
150
+    trees](https://guangchuangyu.github.io/presentation/2016-ggtree-chinar/)
98 151
 
99
-## <i class="fa fa-youtube-play"></i> Video
152
+<i class="fa fa-youtube-play"></i> Video
153
+----------------------------------------
100 154
 
101
-+ [interactive clade highlighting](https://www.youtube.com/watch?v=KcF8Ec38mzI)
102
-+ [interactive rotating clades](https://www.youtube.com/watch?v=lKNn4QlPO0E)
103
-+ [interactive clade labeling](https://www.youtube.com/watch?v=SmcceRD_jxg)
155
+-   [interactive clade
156
+    highlighting](https://www.youtube.com/watch?v=KcF8Ec38mzI)
157
+-   [interactive rotating
158
+    clades](https://www.youtube.com/watch?v=lKNn4QlPO0E)
159
+-   [interactive clade
160
+    labeling](https://www.youtube.com/watch?v=SmcceRD_jxg)
104 161
 
105
-## <i class="fa fa-gift"></i> Workflow
162
+<i class="fa fa-gift"></i> Workflow
163
+-----------------------------------
106 164
 
107
-+ [recreate a tree from a publication (__Bloom__ *et al*, __*Science*__ 2010)](https://rpubs.com/gutijosh9430/124817)
165
+-   [recreate a tree from a publication (**Bloom** *et al*,
166
+    ***Science*** 2010)](https://rpubs.com/gutijosh9430/124817)
... ...
@@ -1,92 +1,118 @@
1
+---
2
+html_preview: False
3
+output:
4
+  md_document:
5
+    variant: markdown
6
+---
7
+
1 8
 <!-- AddToAny BEGIN -->
2 9
 <div class="a2a_kit a2a_kit_size_32 a2a_default_style">
10
+
3 11
 <a class="a2a_dd" href="//www.addtoany.com/share"></a>
4
-<a class="a2a_button_facebook"></a>
5
-<a class="a2a_button_twitter"></a>
12
+<a class="a2a_button_facebook"></a> <a class="a2a_button_twitter"></a>
6 13
 <a class="a2a_button_google_plus"></a>
7
-<a class="a2a_button_pinterest"></a>
8
-<a class="a2a_button_reddit"></a>
9
-<a class="a2a_button_sina_weibo"></a>
10
-<a class="a2a_button_wechat"></a>
14
+<a class="a2a_button_pinterest"></a> <a class="a2a_button_reddit"></a>
15
+<a class="a2a_button_sina_weibo"></a> <a class="a2a_button_wechat"></a>
11 16
 <a class="a2a_button_douban"></a>
17
+
12 18
 </div>
19
+
13 20
 <script async src="//static.addtoany.com/menu/page.js"></script>
14 21
 <!-- AddToAny END -->
15
-
16 22
 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css">
17 23
 
24
+<i class="fa fa-download"></i> Installation
25
+===========================================
18 26
 
19
-# <i class="fa fa-download"></i> Installation
27
+<i class="fa fa-angle-double-right"></i> Could not find function
28
+----------------------------------------------------------------
20 29
 
21
-## <i class="fa fa-angle-double-right"></i> Could not find function
30
+If you got [this
31
+error](https://github.com/GuangchuangYu/ggtree/issues/12), please make
32
+sure you are using the latest R and `ggtree`.
22 33
 
23
-If you got [this error](https://github.com/GuangchuangYu/ggtree/issues/12), please make sure you are using the latest R and `ggtree`.
34
+Packages in Bioconductor, like `ggtree`, have different release policy
35
+compare to CRAN. There are two branches, release and devel, in parallel.
36
+Release branch is more stable and only document improvement and bug
37
+fixes will commit to it. New functions will only commit to `devel`
38
+branch.
24 39
 
25
-Packages in Bioconductor, like `ggtree`, have different release policy compare to CRAN. There are two branches, release and devel, in parallel. Release branch is more stable and only document improvement and bug fixes will commit to it. New functions will only commit to `devel` branch.
40
+Sometimes I may write blog post to introduce new functions which is not
41
+available in `release` branch, you need to install the `devel` version
42
+of `ggtree` in order to use these new functions.
26 43
 
27
-Sometimes I may write blog post to introduce new functions which is not available in `release` branch, you need to install the `devel` version of `ggtree` in order to use these new functions.
44
+You can download the `devel` version of `ggtree` from
45
+<http://bioconductor.org/packages/devel/bioc/html/ggtree.html> and
46
+install it, or install the github version of `ggtree`.
28 47
 
29
-You can download the `devel` version of `ggtree` from [http://bioconductor.org/packages/devel/bioc/html/ggtree.html](http://bioconductor.org/packages/devel/bioc/html/ggtree.html) and install it, or install the github version of `ggtree`.
48
+This also applied to other of my packages, including `GOSemSim`, `DOSE`,
49
+`clusterProfiler`, `ReactomePA` and `ChIPseeker`. If you got the
50
+`could not find function` error, upgrade your installation to latest
51
+release. If the error still exists after upgrading to latest release,
52
+you need to install the devel version.
30 53
 
31
-This also applied to other of my packages, including `GOSemSim`, `DOSE`, `clusterProfiler`, `ReactomePA` and `ChIPseeker`. If you got the `could not find function` error, upgrade your installation to latest release. If the error still exists after upgrading to latest release, you need to install the devel version.
54
+<i class="fa fa-text-height"></i> Text & Label
55
+==============================================
32 56
 
33
-
34
-# <i class="fa fa-text-height"></i> Text & Label
35
-
36
-## <i class="fa fa-angle-double-right"></i> Tip label truncated
57
+<i class="fa fa-angle-double-right"></i> Tip label truncated
58
+------------------------------------------------------------
37 59
 
38 60
 ggplot2 can't auto adjust xlim based on added text.
39 61
 
40
-```r
62
+``` {.r}
41 63
 library(ggtree)
42 64
 ## example tree from https://support.bioconductor.org/p/72398/
43 65
 tree<-read.tree(text="(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);")
44 66
 ggtree(tree) + geom_tiplab()
45 67
 ```
46 68
 
47
-This is because the units are in two different spaces (data and pixel). Users can use xlim to allocate more space for tip label.
69
+This is because the units are in two different spaces (data and pixel).
70
+Users can use xlim to allocate more space for tip label.
48 71
 
49
-```r
72
+``` {.r}
50 73
 ggtree(tree) + geom_tiplab() + xlim(0, 0.06)
51 74
 ```
52 75
 
53
-## <i class="fa fa-angle-double-right"></i> Modify (tip) labels
76
+<i class="fa fa-angle-double-right"></i> Modify (tip) labels
77
+------------------------------------------------------------
54 78
 
55
-This could be easily done via the `%<+%` operator to attach the
56
-modified version of the labels and than use `geom_tiplab` to display
57
-the modified version.
79
+This could be easily done via the `%<+%` operator to attach the modified
80
+version of the labels and than use `geom_tiplab` to display the modified
81
+version.
58 82
 
83
+    raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree")
84
+    raxml <- read.raxml(raxml_file)
59 85
 
60
-```
61
-raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree")
62
-raxml <- read.raxml(raxml_file)
63
-
64
-lb = get.tree(raxml)$tip.label
65
-d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5)))
66
-ggtree(raxml) %<+% d + geom_tiplab(aes(label=label2))
67
-```
86
+    lb = get.tree(raxml)$tip.label
87
+    d = data.frame(label=lb, label2 = paste("AA", substring(lb, 1, 5)))
88
+    ggtree(raxml) %<+% d + geom_tiplab(aes(label=label2))
68 89
 
69 90
 see also
70 91
 [1](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/tFdFgCJ7gQA/tZ6phSgUDQAJ)
71 92
 and [2](https://github.com/GuangchuangYu/ggtree/issues/106).
72 93
 
73
-## <i class="fa fa-angle-double-right"></i> Formatting (tip) labels
94
+<i class="fa fa-angle-double-right"></i> Formatting (tip) labels
95
+----------------------------------------------------------------
74 96
 
75
-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 parsed into expression and displayed as described in `?plotmath`.
97
+If you want to format labels, you need to set `parse=TRUE` in
98
+`geom_text`/`geom_tiplab` and the `label` should be string that can be
99
+parsed into expression and displayed as described in `?plotmath`.
76 100
 
77
-For example, the tiplabels contains two parts, species name and accession number and we want to display species name in _italic_, we can use command like this:
101
+For example, the tiplabels contains two parts, species name and
102
+accession number and we want to display species name in *italic*, we can
103
+use command like this:
78 104
 
79
-```
80
-ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
81
-```
105
+    ggtree(rtree(30)) + geom_tiplab(aes(subset=node==35), label='paste(italic("species name"), "accession number")', parse=T)
82 106
 
83
-## <i class="fa fa-angle-double-right"></i> Avoid overlapping text labels
107
+<i class="fa fa-angle-double-right"></i> Avoid overlapping text labels
108
+----------------------------------------------------------------------
84 109
 
85
-User can use [ggrepel](https://cran.r-project.org/web/packages/ggrepel/) package to repel overlapping text labels.
110
+User can use [ggrepel](https://cran.r-project.org/web/packages/ggrepel/)
111
+package to repel overlapping text labels.
86 112
 
87 113
 For example:
88 114
 
89
-```r
115
+``` {.r}
90 116
 library(ggrepel)
91 117
 library(ggtree)
92 118
 raxml_file <- system.file("extdata/RAxML", "RAxML_bipartitionsBranchLabels.H3", package="ggtree")
... ...
@@ -94,23 +120,36 @@ raxml <- read.raxml(raxml_file)
94 120
 ggtree(raxml) + geom_label_repel(aes(label=bootstrap, fill=bootstrap))
95 121
 ```
96 122
 
97
-For details, please refer to [ggrepel usage examples](https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html).
123
+For details, please refer to [ggrepel usage
124
+examples](https://cran.r-project.org/web/packages/ggrepel/vignettes/ggrepel.html).
98 125
 
99
-## <i class="fa fa-angle-double-right"></i> bootstrap values from newick format
126
+<i class="fa fa-angle-double-right"></i> bootstrap values from newick format
127
+----------------------------------------------------------------------------
100 128
 
101
-It's quite command to store `bootstrap` value as node label in `newick` format. Visualizing node label is easy using `geom_text2(aes(subset = !isTip, label=label))`.
129
+It's quite command to store `bootstrap` value as node label in `newick`
130
+format. Visualizing node label is easy using
131
+`geom_text2(aes(subset = !isTip, label=label))`.
102 132
 
103
-If you want to only display a subset of `bootstrap` (e.g. bootstrap > 80), you can't simply using `geom_text2(subset= (label > 80), label=label)` since `label` is a character vector, which contains node label (bootstrap value) and tip label (taxa name). If we use `geom_text2(subset=(as.numeric(label) > 80), label=label)`, it will also fail since `NAs` were introduced by coercion. We need to convert `NAs` to logical `FALSE`, this can be done by the following code:
133
+If you want to only display a subset of `bootstrap` (e.g. bootstrap &gt;
134
+80), you can't simply using
135
+`geom_text2(subset= (label > 80), label=label)` since `label` is a
136
+character vector, which contains node label (bootstrap value) and tip
137
+label (taxa name). If we use
138
+`geom_text2(subset=(as.numeric(label) > 80), label=label)`, it will also
139
+fail since `NAs` were introduced by coercion. We need to convert `NAs`
140
+to logical `FALSE`, this can be done by the following code:
104 141
 
105
-```r
142
+``` {.r}
106 143
 nwk <- system.file("extdata/RAxML","RAxML_bipartitions.H3", package='ggtree')
107 144
 tr <- read.tree(nwk)
108 145
 ggtree(tr) + geom_text2(aes(label=label, subset = !is.na(as.numeric(label)) & as.numeric(label) > 80))
109 146
 ```
110 147
 
111
-Another solution is converting the bootstrap value outside `ggtree` as I recommended in [google group](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/hiRBjGaAfI0/Y-2zDpvtAwAJ).
148
+Another solution is converting the bootstrap value outside `ggtree` as I
149
+recommended in [google
150
+group](https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/hiRBjGaAfI0/Y-2zDpvtAwAJ).
112 151
 
113
-```r
152
+``` {.r}
114 153
 q <- ggtree(tr)
115 154
 d <- q$data
116 155
 d <- d[!d$isTip,]
... ...
@@ -120,47 +159,58 @@ d <- d[d$label > 80,]
120 159
 q + geom_text(data=d, aes(label=label))
121 160
 ```
122 161
 
162
+<i class="fa fa-map-marker"></i> *aesthetic* mapping
163
+====================================================
123 164
 
124
-# <i class="fa fa-map-marker"></i> _aesthetic_ mapping
125
-
126
-## <i class="fa fa-angle-double-right"></i> inherit _aes_
165
+<i class="fa fa-angle-double-right"></i> inherit *aes*
166
+------------------------------------------------------
127 167
 
128
-```r
168
+``` {.r}
129 169
 ggtree(rtree(30)) + geom_point()
130 170
 ```
131 171
 
132
-For example, we can add symbolic points to nodes with `geom_point()` directly.
133
-The magic here is we don't need to map `x` and `y` position of the points by providing `aes(x, y)` to `geom_point()` since it was already mapped by `ggtree` function and it serves as a global mapping for all layers.
172
+For example, we can add symbolic points to nodes with `geom_point()`
173
+directly. The magic here is we don't need to map `x` and `y` position of
174
+the points by providing `aes(x, y)` to `geom_point()` since it was
175
+already mapped by `ggtree` function and it serves as a global mapping
176
+for all layers.
134 177
 
135
-But what if we provide a `dataset` in a layer and the `dataset` doesn't contain column of `x` and/or `y`,
136
-the layer function also try to map `x` and `y` and also others if you map them in `ggtree` function.
137
-As these variable is not available in your `dataset`, you will get the following error:
178
+But what if we provide a `dataset` in a layer and the `dataset` doesn't
179
+contain column of `x` and/or `y`, the layer function also try to map `x`
180
+and `y` and also others if you map them in `ggtree` function. As these
181
+variable is not available in your `dataset`, you will get the following
182
+error:
138 183
 
139
-```
140
-Error in eval(expr, envir, enclos) : object 'x' not found
141
-```
184
+    Error in eval(expr, envir, enclos) : object 'x' not found
142 185
 
143
-This can be fixed by using parameter `inherit.aes=FALSE` which will disable inheriting mapping from `ggtree` function.
186
+This can be fixed by using parameter `inherit.aes=FALSE` which will
187
+disable inheriting mapping from `ggtree` function.
144 188
 
145
-## <i class="fa fa-angle-double-right"></i> use `$` in aes
189
+<i class="fa fa-angle-double-right"></i> use `$` in aes
190
+-------------------------------------------------------
146 191
 
147 192
 NEVER DO THIS.
148 193
 
149
-see the explaination in the [ggplot2 book 2ed](https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes):
194
+see the explaination in the [ggplot2 book
195
+2ed](https://github.com/hadley/ggplot2-book/blob/master/layers.rmd#aesthetic-mappings-secaes):
150 196
 
151
->Never refer to a variable with `$` (e.g., `diamonds$carat`) in `aes()`. This breaks containment, so that the plot no longer contains everything it needs, and causes problems if ggplot2 changes the order of the rows, as it does when facetting.
197
+> Never refer to a variable with `$` (e.g., `diamonds$carat`) in
198
+> `aes()`. This breaks containment, so that the plot no longer contains
199
+> everything it needs, and causes problems if ggplot2 changes the order