# ggtree

**Repository Path**: GuangchuangYu/ggtree

## Basic Information

- **Project Name**: ggtree
- **Description**: Visualization and annotation of phylogenetic trees
- **Primary Language**: R
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 1
- **Forks**: 0
- **Created**: 2017-07-25
- **Last Updated**: 2022-11-06

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

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

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

<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)
[![](https://img.shields.io/badge/release%20version-3.4.2-green.svg)](https://www.bioconductor.org/packages/ggtree)
[![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree)
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` r badge_devel("guangchuangyu/ggtree", "green")`
` r badge_bioc_download("ggtree", "total", "blue")`
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` r badge_bioc_download_rank("ggtree")`
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‘ggtree’ extends the ‘ggplot2’ plotting system which implemented the
grammar of graphics. ‘ggtree’ is designed for visualization and
annotation of phylogenetic trees and other tree-like structures with
their annotation data.

## :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)
[![](https://img.shields.io/badge/follow%20me%20on-WeChat-green.svg)](https://guangchuangyu.github.io/blog_images/biobabble.jpg)

If you use [ggtree](http://bioconductor.org/packages/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**<sup>\*</sup>, TTY Lam, H Zhu, Y Guan<sup>\*</sup>. 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<sup>\*</sup>. 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).