ggtree
an R package for visualization of tree and annotation data
Bioconductor version: Release (3.19)
'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")):
Installation
To install this package, start R (version "4.4") 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 | 3.12.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.5.0) |
| Imports | ape, aplot, dplyr, ggplot2 (> 3.3.6), grid, magrittr, methods, purrr, rlang, ggfun (>= 0.0.9), yulab.utils, tidyr, tidytree (>= 0.4.5), treeio(>= 1.8.0), utils, scales, stats, cli |
| 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
| Suggests | emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, testthat, tibble, glue |
| Linking To | |
| Enhances | |
| Depends On Me | ggtreeDendro, tanggle |
| Imports Me | LinTInd, LymphoSeq, MicrobiotaProcess, cardelino, cogeqc, enrichplot, gINTomics, ggmsa, ggtreeExtra, ggtreeSpace, miaViz, microbiomeMarker, orthogene, philr, scBubbletree, singleCellTK, sitePath, systemPipeTools, treeclimbR, treekoR, DAISIEprep, ddtlcm, dowser, EvoPhylo, FossilSim, genBaRcode, harrietr, numbat, Platypus, RevGadgets, scistreer, shinyTempSignal, STraTUS, Sysrecon |
| Suggests Me | TreeAndLeaf, TreeSummarizedExperiment, compcodeR, syntenet, treeio, universalmotif, aplot, aplotExtra, CoOL, DAISIE, deeptime, gggenomes, ggimage, ggtangle, idiogramFISH, MetaNet, nosoi, oppr, PCMBase, pctax, RAINBOWR, rhierbaps, rphylopic |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ggtree_3.12.0.tar.gz |
| Windows Binary (x86_64) | ggtree_3.12.0.zip |
| macOS Binary (x86_64) | ggtree_3.12.0.tgz |
| macOS Binary (arm64) | ggtree_3.12.0.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 |