ggtree
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see ggtree.
an R package for visualization of tree and annotation data
Bioconductor version: 3.14
'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] , Yonghe Xia [ctb], Justin Silverman [ctb], Bradley Jones [ctb], Watal M. Iwasaki [ctb], Ruizhu Huang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu at gmail.com>
citation("ggtree")):
Installation
To install this package, start R (version "4.1") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | 3.2.1 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | ape, aplot (>= 0.0.4), dplyr, ggplot2 (>= 3.0.0), grid, magrittr, methods, purrr, rlang, ggfun, yulab.utils, tidyr, tidytree (>= 0.2.6), treeio(>= 1.8.0), utils, scales |
| System Requirements | |
| URL | https://yulab-smu.top/treedata-book/(book) http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628(paper) |
| Bug Reports | https://github.com/YuLab-SMU/ggtree/issues |
See More
| Suggests | emojifont, ggimage, ggplotify, grDevices, knitr, prettydoc, rmarkdown, stats, testthat, tibble |
| Linking To | |
| Enhances | |
| Depends On Me | tanggle |
| Imports Me | enrichplot, ggtreeExtra, LymphoSeq, miaViz, microbiomeMarker, MicrobiotaProcess, philr, singleCellTK, sitePath, systemPipeTools, treekoR |
| Suggests Me | ggmsa, TreeAndLeaf, treeio, TreeSummarizedExperiment, universalmotif |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ggtree_3.2.1.tar.gz |
| Windows Binary | ggtree_3.2.1.zip |
| macOS 10.13 (High Sierra) | ggtree_3.2.1.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 |
| Old Source Packages for BioC 3.14 | Source Archive |