ggtree

This is the released version of ggtree; for the devel version, see ggtree.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

an R package for visualization of tree and annotation data

Bioconductor version: Release (3.23)

'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] ORCID: 0000-0002-6485-8781 , Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] ORCID: 0000-0003-3513-5362 , Lin Li [ctb], Bradley Jones [ctb], Justin Silverman [ctb], Watal M. Iwasaki [ctb], Yonghe Xia [ctb], Ruizhu Huang [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

Citation (from within R, enter citation("ggtree")):

Guangchuang Yu, Tommy Tsan-Yuk Lam, Shuangbin Xu. ggtree: an R package for visualization of tree and annotation data. doi:10.18129/B9.bioc.ggtree, R package version 4.2.0, https://bioconductor.org/packages/ggtree.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

ggtree	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization
Version	4.2.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	ape, aplot, cli, dplyr, ggfun (>= 0.1.7), ggiraph (>= 0.9.1), ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, scales, stats, tidyr, tidytree (>= 0.4.5), treeio (>= 1.8.0), utils, yulab.utils (>= 0.2.3)
System Requirements
URL	https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/ (book) http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628 (paper)
Bug Reports	https://github.com/YuLab-SMU/ggtree/issues

Suggests	emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, igraph, testthat, tibble, glue, Biostrings
Linking To
Enhances
Depends On Me	ggtreeDendro, tanggle
Imports Me	BioVizSeq, cardelino, cellmig, cogeqc, crumblr, DAISIEprep, ddtlcm, delimtools, dowser, DspikeIn, enrichplot, EvoPhylo, genBaRcode, ggmsa, ggtreeExtra, ggtreeSpace, gINTomics, harrietr, iSEEtree, lefser, LymphoSeq, MetaboDynamics, miaViz, MicrobiotaProcess, mitology, mycolorsTB, numbat, orthogene, philr, Rclade, RevGadgets, scBubbletree, scDotPlot, scistreer, SEMPLR, shinyTempSignal, singleCellTK, sitePath, STraTUS, SVP, Sysrecon, systemPipeTools, TransProR, treeclimbR, treekoR
Suggests Me	aplot, aplotExtra, bGMYC4, compcodeR, CrcBiomeScreen, DAISIE, deeptime, epiSeeker, fastreeR, FossilSim, gggenomes, ggimage, ggtangle, idiogramFISH, MetaNet, nosoi, OMA, oppr, PCMBase, pctax, piglet, RAINBOWR, rhierbaps, rphylopic, syntenet, TreeAndLeaf, treeio, treestructure, TreeSummarizedExperiment, universalmotif
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	ggtree_4.2.0.tar.gz
Windows Binary (x86_64)	ggtree_4.2.0.zip
macOS Binary (big-sur-x86_64)	ggtree_4.2.0.tgz
macOS Binary (sonoma-arm64)	ggtree_4.2.0.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