README.Rmd

---
output:
  md_document:
    variant: gfm
html_preview: false
---

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


#  ggtree: an R package for visualization of phylogenetic trees with their annotation 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)
}

```

<a href="https://yulab-smu.github.io/treedata-book/"><img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /></a>

[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
`r badge_bioc_release("ggtree", "green")`
[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
[![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)



<!--
[![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)
[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
[![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

` r badge_devel("guangchuangyu/ggtree", "green")`
` r badge_bioc_download("ggtree", "total", "blue")`
` r badge_bioc_download("ggtree", "month", "blue")`
` r badge_bioc_download_rank("ggtree")`
-->

```{r comment="", echo=FALSE, results='asis'}
cat(packageDescription('ggtree')$Description)
```




## :writing_hand: Authors

Guangchuang YU

School of Basic Medical Sciences, Southern Medical University

<https://yulab-smu.top>

[![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', 'WeChat', 'green', 'https://guangchuangyu.github.io/blog_images/biobabble.jpg')`



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

1. S Xu, L Li, X Luo, M Chen, W Tang, L Zhan, Z Dai, TT. Lam, Y Guan, __G Yu__. Ggtree: A serialized data object for visualization of a phylogenetic tree and annotation data. __*iMeta*__, 2022, 1(4):e56. doi: [10.1002/imt2.56](https://doi.org/10.1002/imt2.56)
2. __G Yu__. Data Integration, Manipulation and Visualization of Phylogenetic Treess (1st edition). __*Chapman and Hall/CRC*__, 2022. doi: [10.1201/9781003279242](https://doi.org/10.1201/9781003279242)
3. __G Yu__. Using ggtree to visualize data on tree-like structures. __*Current Protocols in Bioinformatics*__, 2020, 69:e96. doi: [10.1002/cpbi.96](https://doi.org/10.1002/cpbi.96)
   - [Source code and data to reproduce figures in the article](https://github.com/GuangchuangYu/ggtree-current-protocols)
4. __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)
5. __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)


<center>
<a href="https://www.routledge.com/Data-Integration-Manipulation-and-Visualization-of-Phylogenetic-Trees/Yu/p/book/9781032233574"><img src="https://yulab-smu.top/treedata-book/9781032233574_cover_review.png" style="width:500px;border:2px solid black;"/></a>
</center>


## :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).