ggtree

DOI: 10.18129/B9.bioc.ggtree    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see ggtree.

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

Bioconductor version: 3.7

'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], 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:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("ggtree")

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 1.12.7
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 (>= 2.2.1.9000), grDevices, grid, magrittr, methods, purrr, rlang, rvcheck (>= 0.1.0), scales, tibble, tidyr, tidytree (>= 0.1.5), 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
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_1.12.7.tar.gz
Windows Binary ggtree_1.12.7.zip
Mac OS X 10.11 (El Capitan) ggtree_1.12.7.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

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