To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")
In most cases, you don't need to download the package archive at all.
ggtree
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an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
Bioconductor version: Release (3.5)
'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.
Author: Guangchuang Yu [aut, cre, cph], Tommy Tsan-Yuk Lam [aut, ths], Justin Silverman [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
Citation (from within R,
enter citation("ggtree")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")
Documentation
| HTML | R Script | 00 ggtree introduction |
| HTML | R Script | 01 Tree Data Import |
| HTML | R Script | 02 Tree Visualization |
| HTML | R Script | 03 Tree Manipulation |
| HTML | R Script | 04 Tree Annotation |
| HTML | R Script | 05 Advance Tree Annotation |
| HTML | R Script | 06 ggtree utilities |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization |
| Version | 1.8.2 |
| In Bioconductor since | BioC 3.1 (R-3.2) (2.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3.2), ggplot2 (>= 2.2.0), treeio |
| Imports | ape, grDevices, grid, magrittr, methods, rvcheck, tidyr, utils |
| LinkingTo | |
| Suggests | Biostrings, colorspace, EBImage, emojifont, knitr, prettydoc, rmarkdown, scales, testthat |
| SystemRequirements | |
| Enhances | |
| URL | https://guangchuangyu.github.io/ggtree |
| BugReports | https://github.com/GuangchuangYu/ggtree/issues |
| Depends On Me | |
| Imports Me | LINC, LymphoSeq, philr |
| Suggests Me | treeio |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ggtree_1.8.2.tar.gz |
| Windows Binary | ggtree_1.8.2.zip |
| Mac OS X 10.11 (El Capitan) | ggtree_1.8.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ggtree |
| Package Short Url | http://bioconductor.org/packages/ggtree/ |
| Package Downloads Report | Download Stats |
Documentation »
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