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 <!-- README.md is generated from README.Rmd. Please edit that file -->
 
 

 #  ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

 
 ```{r echo=FALSE, results="hide", message=FALSE}

 #library("txtplot")

 library("badger")

 library("ypages")

 library("ggplot2")

 library("yyplot")

 ```
 

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

 `r badge_bioc_release("ggtree", "green")`

 `r badge_devel("guangchuangyu/ggtree", "green")`

 [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)

 `r badge_bioc_download("ggtree", "total", "blue")`
 `r badge_bioc_download("ggtree", "month", "blue")`

 
 [![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-`r gsub('-', '--', Sys.Date())`-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)
 
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
 [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree)
 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)

 [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)
 [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
 
 [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
 

 
 For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.
 
 + [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)
 + [FAQ](https://guangchuangyu.github.io/ggtree/faq/)
 + [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)
 + [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)
 
 

 -----------------------------------------------------
 
 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.
 

 
 `r badge_doi("10.1111/2041-210X.12628", "green")`
 `r badge_altmetric("10533079", "green")`

 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`
 

 
 ----------------------------------------------------------------------------------------
 
 
 ### Citation
 
 
 ```{r echo=F, comment=NA}

 p <- plot_citation_trend('DO5oG40AAAAJ', 'HtEfBTGE9r8C')
 ggsave(p, file="docs/images/citation.png", width=8, height=4)

 ```
 

 <img src="docs/images/citation.png" width="890"/>

 ### Download stats
 

 `r badge_download_bioc("ggtree")`

 `r badge_bioc_download("ggtree", "total", "blue")`
 `r badge_bioc_download("ggtree", "month", "blue")`

 ```{r echo=F, message=F, comment=NA}

 x <- dlstats::bioc_stats("ggtree")
 x <- x[-nrow(x), ] # last month data is not complete

 ## txtplot(ggtree::Date2decimal(x$end), x$Nb_of_downloads, width=100, height=25)
 p <- ggplot(x, aes(end, Nb_of_distinct_IPs)) + geom_point() + geom_line() +
     theme_minimal() +xlab(NULL) + ylab(NULL) +
     labs(title="ggtree", subtitle="Monthly download stats (distinct IPs)", caption="data from Bioconductor")

 ggsave(p, file="docs/images/dlstats.png", width=8, height=4)

 ```
 

 <img src="docs/images/dlstats.png" width="890"/>

 ## Contributors
 
 This project exists thanks to all the people who contribute. [[Contribute]](CONTRIBUTING.md).

 <a href="https://github.com/GuangchuangYu/ggtree/graphs/contributors"><img src="https://opencollective.com/ggtree/contributors.svg?width=890" /></a>

 
 
 ## Backers
 
 Thank you to all our backers! 🙏 [[Become a backer](https://opencollective.com/ggtree#backer)]
 
 <a href="https://opencollective.com/ggtree#backers" target="_blank"><img src="https://opencollective.com/ggtree/backers.svg?width=890"></a>
 
 
 ## Sponsors
 
 Support this project by becoming a sponsor. Your logo will show up here with a link to your website. [[Become a sponsor](https://opencollective.com/ggtree#sponsor)]
 
 <a href="https://opencollective.com/ggtree/sponsor/0/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/0/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/1/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/1/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/2/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/2/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/3/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/3/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/4/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/4/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/5/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/5/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/6/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/6/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/7/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/7/avatar.svg"></a>
 <a href="https://opencollective.com/ggtree/sponsor/8/website" target="_blank"><img src="https://opencollective.com/ggtree/sponsor/8/avatar.svg"></a>
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