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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 days ago
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:christmas_tree:Visualization and annotation of phylogenetic trees
- Host: GitHub
- URL: https://github.com/YuLab-SMU/ggtree
- Owner: YuLab-SMU
- Created: 2014-12-03T05:23:47.000Z (almost 10 years ago)
- Default Branch: devel
- Last Pushed: 2024-10-24T08:31:21.000Z (23 days ago)
- Last Synced: 2024-10-30T00:37:43.777Z (17 days ago)
- Topics: annotations, ggplot2, phylogenetic-trees, r, visualization
- Language: R
- Homepage: https://yulab-smu.top/contribution-tree-data/
- Size: 16.1 MB
- Stars: 839
- Watchers: 37
- Forks: 174
- Open Issues: 165
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS
- Contributing: CONTRIBUTING.md
Awesome Lists containing this project
README
---
output:
md_document:
variant: gfm
html_preview: false
---
# 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)
}
```
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
`r badge_bioc_release("ggtree", "green")`
[](https://codecov.io/gh/GuangchuangYu/ggtree)
[](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
[](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)
`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).