ggtree

DOI: 10.18129/B9.bioc.ggtree    

an R package for visualization of tree and annotation data

Bioconductor version: Release (3.10)

'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>

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

Installation

To install this package, start R (version "3.6") 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 2.0.0
In Bioconductor since BioC 3.1 (R-3.2) (4.5 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports ape, 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, 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_2.0.0.tar.gz
Windows Binary ggtree_2.0.0.zip
Mac OS X 10.11 (El Capitan) ggtree_2.0.0.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

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