Welcome to the new bioconductor.org!

ggtree

an R package for visualization of tree and annotation data


Bioconductor version: Release (3.18)

'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], Shuangbin Xu [aut] , 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")):

Installation

To install this package, start R (version "4.3") 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

Details

biocViews Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization
Version 3.10.1
In Bioconductor since BioC 3.1 (R-3.2) (9 years)
License Artistic-2.0
Depends R (>= 3.5.0)
Imports ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.9), yulab.utils, tidyr, tidytree (>= 0.4.5), treeio(>= 1.8.0), utils, scales, stats, cli
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
See More
Suggests emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue
Linking To
Enhances
Depends On Me ggtreeDendro, tanggle
Imports Me cardelino, cogeqc, enrichplot, ggmsa, ggtreeExtra, LinTInd, LymphoSeq, miaViz, microbiomeMarker, MicrobiotaProcess, orthogene, philr, scBubbletree, singleCellTK, sitePath, systemPipeTools, treekoR
Suggests Me compcodeR, syntenet, TreeAndLeaf, treeio, TreeSummarizedExperiment, universalmotif
Links To Me
Build Report Build Report

Package Archives

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

Source Package ggtree_3.10.1.tar.gz
Windows Binary ggtree_3.10.1.zip
macOS Binary (x86_64) ggtree_3.10.1.tgz
macOS Binary (arm64) ggtree_3.10.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggtree
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggtree
Bioc Package Browser https://code.bioconductor.org/browse/ggtree/
Package Short Url https://bioconductor.org/packages/ggtree/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive