ggtree

DOI: 10.18129/B9.bioc.ggtree    

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

Bioconductor version: Release (3.8)

'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], Bradley Jones [ctb], Watal M. Iwasaki [ctb]

Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ggtree", version = "3.8")

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 1.14.2
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 (>= 3.0.0), grDevices, grid, magrittr, methods, purrr, rlang, rvcheck (>= 0.1.0), scales, tibble, tidyr, tidytree (>= 0.1.9), 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, universalmotif
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_1.14.2.tar.gz
Windows Binary ggtree_1.14.2.zip
Mac OS X 10.11 (El Capitan) ggtree_1.14.2.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
Old Source Packages for BioC 3.8 Source Archive

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