<!-- 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> [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://www.bioconductor.org/packages/ggtree) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://awesome-r.com/#awesome-r-graphic-displays) <!-- [](http://www.repostatus.org/#active) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](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")` --> ‘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> [](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu) [](https://saythanks.io/to/GuangchuangYu) [](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**^\*, 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).