ggtree

DOI: 10.18129/B9.bioc.ggtree    

an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

Bioconductor version: Release (3.6)

'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>

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
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
Version	1.10.5
In Bioconductor since	BioC 3.1 (R-3.2) (3 years)
License	Artistic-2.0
Depends	R (>= 3.3.2), ggplot2 (>= 2.2.0), treeio
Imports	ape, grDevices, grid, magrittr, methods, rvcheck, scales, tidyr, utils
LinkingTo
Suggests	Biostrings, colorspace, EBImage, emojifont, knitr, prettydoc, rmarkdown, 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_1.10.5.tar.gz
Windows Binary	ggtree_1.10.5.zip
Mac OS X 10.11 (El Capitan)	ggtree_1.10.5.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ggtree
Package Short Url	http://bioconductor.org/packages/ggtree/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive