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https://github.com/YuLab-SMU/ggtree

:christmas_tree:Visualization and annotation of phylogenetic trees
https://github.com/YuLab-SMU/ggtree

annotations ggplot2 phylogenetic-trees r visualization

Last synced: 2 months ago
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:christmas_tree:Visualization and annotation of phylogenetic trees

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README 

        
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#  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)

}



```






[![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)



```{r comment="", echo=FALSE, results='asis'}

cat(packageDescription('ggtree')$Description)

```



## :writing_hand: Authors



Guangchuang YU



School of Basic Medical Sciences, Southern Medical University



[![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)






## :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).