ggtree

DOI: 10.18129/B9.bioc.ggtree    

an R package for visualization of tree and annotation data

Bioconductor version: Release (3.11)

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

Author: Guangchuang Yu [aut, cre, cph] , Tommy Tsan-Yuk Lam [aut, ths], Justin Silverman [ctb], Bradley Jones [ctb], Watal M. Iwasaki [ctb], Ruizhu Huang [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ggtree")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("ggtree")

 

HTML	R Script	ggtree
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization
Version	2.2.4
In Bioconductor since	BioC 3.1 (R-3.2) (5.5 years)
License	Artistic-2.0
Depends	R (>= 3.5.0)
Imports	ape, aplot (>= 0.0.4), dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, rvcheck, tidyr, tidytree (>= 0.2.6), treeio(>= 1.8.0), utils
LinkingTo
Suggests	emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, scales, stats, testthat, tibble
SystemRequirements
Enhances
URL	https://yulab-smu.github.io/treedata-book/
BugReports	https://github.com/YuLab-SMU/ggtree/issues
Depends On Me
Imports Me	LINC, LymphoSeq, MicrobiotaProcess, philr, singleCellTK, universalmotif
Suggests Me	metagenomeFeatures, treeio, TreeSummarizedExperiment
Links To Me
Build Report

Package Archives

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

Source Package	ggtree_2.2.4.tar.gz
Windows Binary	ggtree_2.2.4.zip
macOS 10.13 (High Sierra)	ggtree_2.2.4.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	https://bioconductor.org/packages/ggtree/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.11	Source Archive