ggtree

DOI: 10.18129/B9.bioc.ggtree    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ggtree.

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

Bioconductor version: 3.7

'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] (<https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [aut, ths], Justin Silverman [ctb], Watal M. Iwasaki [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

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("ggtree")

 

HTML	R Script	01 ggtree Introduction
HTML	R Script	02 Tree Visualization
HTML	R Script	03 Tree Manipulation
HTML	R Script	04 Tree Annotation
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
Version	1.12.7
In Bioconductor since	BioC 3.1 (R-3.2) (3.5 years)
License	Artistic-2.0
Depends	R (>= 3.4.0)
Imports	ape, dplyr, ggplot2 (>= 2.2.1.9000), grDevices, grid, magrittr, methods, purrr, rlang, rvcheck (>= 0.1.0), scales, tibble, tidyr, tidytree (>= 0.1.5), treeio(>= 1.3.14), utils
LinkingTo
Suggests	colorspace, cowplot, emojifont, ggimage, knitr, prettydoc, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://guangchuangyu.github.io/software/ggtree
BugReports	https://github.com/GuangchuangYu/ggtree/issues
Depends On Me
Imports Me	LINC, LymphoSeq, philr, singleCellTK
Suggests Me	metagenomeFeatures, treeio
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	ggtree_1.12.7.tar.gz
Windows Binary	ggtree_1.12.7.zip
Mac OS X 10.11 (El Capitan)	ggtree_1.12.7.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ggtree
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ggtree
Package Short Url	http://bioconductor.org/packages/ggtree/
Package Downloads Report	Download Stats