ggtree

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

an R package for visualization of tree and annotation data

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DOI: 10.18129/B9.bioc.ggtree

Bioconductor version: Development (3.23)

'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] ORCID iD ORCID: 0000-0002-6485-8781 , Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] ORCID iD ORCID: 0000-0003-3513-5362 , 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 "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization

Version 4.1.1

In Bioconductor since BioC 3.1 (R-3.2) (10.5 years)

License Artistic-2.0

Depends R (>= 4.2.0)

Imports ape, aplot, dplyr, ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.1.7), yulab.utils (>= 0.1.6), tidyr, tidytree (>= 0.4.5), treeio(>= 1.8.0), utils, scales, stats, cli, ggiraph (>= 0.9.1)

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

Suggests emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue, Biostrings

Linking To

Enhances

Depends On Me ggtreeDendro, tanggle