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#  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")
Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}

```

<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)
[![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)
[![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)



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.



For details, please visit our project website, <https://guangchuangyu.github.io/software/ggtree>.

+ [Documentation](https://guangchuangyu.github.io/software/ggtree/documentation/)
+ [FAQ](https://guangchuangyu.github.io/software/ggtree/faq/)
+ [Featured Articles](https://guangchuangyu.github.io/software/ggtree/featuredArticles/)
+ [Feedback](https://guangchuangyu.github.io/software/ggtree/#feedback)


## :writing_hand: Authors

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

<https://guangchuangyu.github.io>

[![Twitter](https://img.shields.io/twitter/url/http/shields.io.svg?style=social&logo=twitter)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)
[![saythanks](https://img.shields.io/badge/say-thanks-ff69b4.svg)](https://saythanks.io/to/GuangchuangYu)
`r badger::badge_custom('follow me on', '微信', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`
`r badger::badge_custom('打赏', '支付宝/微信', 'green', 'https://guangchuangyu.github.io/blog_images/pay_qrcode.png')`



If you use `r Biocpkg('ggtree')` in published research, please cite the most appropriate paper(s) from this list:

1. __G Yu__^\*^, TTY Lam, H Zhu, Y Guan^\*^. Two methods for mapping and visualizing associated data on phylogeny using ggtree. __*Molecular Biology and Evolution*__, 2018, 35(2):3041-3043.
doi: [10.1093/molbev/msy194](https://doi.org/10.1093/molbev/msy194).
     - [Source code to produce Supplementary Material](https://github.com/GuangchuangYu/plotting_tree_with_data)
2. __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.
doi: [10.1111/2041-210X.12628](https://doi.org/10.1111/2041-210X.12628).



<img src="https://guangchuangyu.github.io/software/citation_trend/ggtree.png" width="890"/>



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


<img src="https://guangchuangyu.github.io/software/dlstats/ggtree.png" width="890"/>



## :sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to
abide by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).