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.

ggtree: a phylogenetic tree viewer for different types of tree annotations

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

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
• updating a tree view using %<% operator
• an example of drawing beast tree using ggtree
• flip and rotate branches in ggtree
• ggtree with funny fonts
• annotate phylogenetic tree with local images

To view the vignette of ggtree installed in your system, start R and enter:

vignette("ggtree", package = "ggtree")

Bugs/Feature requests

• If you have any, let me know. Thx!