ggtree

DOI: 10.18129/B9.bioc.ggtree    

This is the development version of ggtree; for the stable release version, see ggtree.

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

Bioconductor version: Development (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]

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

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 1.11.5
In Bioconductor since BioC 3.1 (R-3.2) (3 years)
License Artistic-2.0
Depends R (>= 3.4.0)
Imports ape, dplyr, ggplot2 (>= 2.2.0), grDevices, grid, magrittr, methods, rvcheck, scales, tibble, tidyr, tidytree (>= 0.1.5), treeio(>= 1.3.9), utils
LinkingTo
Suggests colorspace, cowplot, emojifont, ggimage, knitr, prettydoc, rmarkdown, testthat
SystemRequirements
Enhances
URL https://guangchuangyu.github.io/ggtree
BugReports https://github.com/GuangchuangYu/ggtree/issues
Depends On Me
Imports Me LINC, LymphoSeq, philr, roma
Suggests Me treeio
Build Report  

Package Archives

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

Source Package ggtree_1.11.5.tar.gz
Windows Binary ggtree_1.11.5.zip
Mac OS X 10.11 (El Capitan) ggtree_1.11.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/ggtree
Package Short Url http://bioconductor.org/packages/ggtree/
Package Downloads Report Download Stats

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