https://github.com/trinker/ggtree-1
This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/ggtree.html Contributions: https://github.com/GuangchuangYu/ggtree. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=ggtree or https://github.com/GuangchuangYu/ggtree/issues.
https://github.com/trinker/ggtree-1
Last synced: 5 days ago
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This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/ggtree.html Contributions: https://github.com/GuangchuangYu/ggtree. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=ggtree or https://github.com/GuangchuangYu/ggtree/issues.
- Host: GitHub
- URL: https://github.com/trinker/ggtree-1
- Owner: trinker
- Created: 2015-09-03T12:50:15.000Z (almost 11 years ago)
- Default Branch: master
- Last Pushed: 2015-09-03T08:11:58.000Z (almost 11 years ago)
- Last Synced: 2025-04-08T16:13:58.860Z (about 1 year ago)
- Language: R
- Homepage:
- Size: 889 KB
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# ggtree: a phylogenetic tree viewer for different types of tree annotations
[](http://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives)
[](http://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)
[](http://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since)
[](https://support.bioconductor.org/t/ggtree/)
[](http://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source)
[](http://bioconductor.org/packages/stats/bioc/ggtree.html)
The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`.
`ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data in the tree.
## Authors ##
Guangchuang Yu and Tommy Tsan-Yuk Lam, School of Public Health, The University of Hong Kong.
## Citation ##
Please cite the following article when using `ggtree`:
```
G Yu, D Smith, H Zhu, Y Guan, TTY Lam,
ggtree: an R package for visualization and annotation of phylogenetic tree
with different types of meta-data.
Methods in Ecology and Evolution, submitted
```
## License ##
All source code is copyright, under the Artistic-2.0 License.
For more information on Artistic-2.0 License see [http://opensource.org/licenses/Artistic-2.0](http://opensource.org/licenses/Artistic-2.0)
## Installation ##
To install:
* the latest released version: `biocLite("ggtree")`
* the latest development version: `install_github("GuangchuangYu/ggtree")`
## Documentation ##
+ [viewing and annotating phylogenetic tree with ggtree](http://ygc.name/2014/12/21/ggtree/)
+ [updating a tree view using %<% operator](http://ygc.name/2015/02/10/ggtree-updating-a-tree-view/)
+ [an example of drawing beast tree using ggtree](http://ygc.name/2015/04/01/an-example-of-drawing-beast-tree-using-ggtree/)
+ [flip and rotate branches in ggtree](http://ygc.name/2015/07/01/flip-and-rotate-branches-in-ggtree/)
+ [ggtree with funny fonts](http://ygc.name/2015/06/12/ggtree-with-funny-fonts/)
+ [annotate phylogenetic tree with local images](http://ygc.name/2015/08/01/ggtree-annotate-phylogenetic-tree-with-local-images/)
To view the vignette of `ggtree` installed in your system, start `R` and enter:
```r
vignette("ggtree", package = "ggtree")
```
## Bugs/Feature requests ##
- If you have any, [let me know](https://github.com/GuangchuangYu/ggtree/issues). Thx!