ggtree
an R package for visualization of tree and annotation data
Bioconductor version: 3.23 · Package version: 4.2.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
'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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ggtree")Details
| Maintainer | Guangchuang Yu <guangchuangyu@gmail.com> |
| Author | Guangchuang Yu [aut, cre, cph] (ORCID: <https://orcid.org/0000-0002-6485-8781>), Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] (ORCID: <https://orcid.org/0000-0003-3513-5362>), Lin Li [ctb], Bradley Jones [ctb], Justin Silverman [ctb], Watal M. Iwasaki [ctb], Yonghe Xia [ctb], Ruizhu Huang [ctb] |
| License | Artistic-2.0 |
| 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 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization |
| Package Short Url | https://bioconductor.org/packages/ggtree/ |
Citation
From within R, enter citation("ggtree"):
Guangchuang Yu, Tommy Tsan-Yuk Lam, Shuangbin Xu. ggtree: an R package for visualization of tree and annotation data. doi:10.18129/B9.bioc.ggtree, R package version 4.2.0, https://bioconductor.org/packages/ggtree.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | ggtree_4.2.0.tar.gz |
| Windows binary (x86_64) | ggtree_4.2.0.zip |
| macOS binary (arm64) | ggtree_4.2.0.tgz |
| macOS binary (x86_64) | ggtree_4.2.0.tgz |
Dependencies
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)
Suggests: emojifont, ggimage, ggplotify, shadowtext, grDevices, knitr, prettydoc, rmarkdown, igraph, testthat, tibble, glue, Biostrings
Reverse dependencies
Depends On Me (2): ggtreeDendro, tanggle
Imports Me (45): BioVizSeq, cardelino, cellmig, cogeqc, crumblr, DAISIEprep, ddtlcm, delimtools, dowser, DspikeIn, enrichplot, EvoPhylo, genBaRcode, ggmsa, ggtreeExtra, ggtreeSpace, gINTomics, harrietr, iSEEtree, lefser, LymphoSeq, MetaboDynamics, miaViz, MicrobiotaProcess, mitology, mycolorsTB, numbat, orthogene, philr, Rclade, RevGadgets, scBubbletree, scDotPlot, scistreer, SEMPLR, shinyTempSignal, singleCellTK, sitePath, STraTUS, SVP, Sysrecon, systemPipeTools, TransProR, treeclimbR, treekoR
Suggests Me (29): aplot, aplotExtra, bGMYC4, compcodeR, CrcBiomeScreen, DAISIE, deeptime, epiSeeker, fastreeR, FossilSim, gggenomes, ggimage, ggtangle, idiogramFISH, MetaNet, nosoi, oppr, PCMBase, pctax, piglet, RAINBOWR, rhierbaps, rphylopic, syntenet, TreeAndLeaf, treeio, treestructure, TreeSummarizedExperiment, universalmotif