ggtree
an R package for visualization of tree and annotation data
Bioconductor version: 3.23 · Package version: 4.2.0
'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 |
| Downloads rank | 32590 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, Annotation, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization |
Documentation
Download
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 (44): 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, RevGadgets, scBubbletree, scDotPlot, scistreer, SEMPLR, shinyTempSignal, singleCellTK, sitePath, STraTUS, SVP, Sysrecon, systemPipeTools, TransProR, treeclimbR, treekoR
Suggests Me (28): aplot, aplotExtra, 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