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
Bioconductor version: Development (3.24)
'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], Shuangbin Xu [aut]
, 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("ggtree")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization |
| Version | 4.3.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 4.2.0) |
| Imports | ape, aplot, cli, dplyr, ggfun (>= 0.1.7), ggiraph (>= 0.9.1), ggplot2 (>= 4.0.0), grid, magrittr, methods, purrr, rlang, scales, stats, tidyr, tidytree (>= 0.4.5), treeio(>= 1.8.0), utils, yulab.utils (>= 0.2.3) |
| 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 |
See More
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ggtree_4.3.0.tar.gz |
| Windows Binary (x86_64) | ggtree_4.3.0.zip |
| macOS Binary (big-sur-x86_64) | ggtree_4.3.0.tgz |
| macOS Binary (sonoma-arm64) | ggtree_4.3.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ggtree |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ggtree |
| Bioc Package Browser | https://code.bioconductor.org/browse/ggtree/ |
| Package Short Url | https://bioconductor.org/packages/ggtree/ |
| Package Downloads Report | Download Stats |