ggtree

This is thereleased version of ggtree; for the devel version, seeggtree.

an R package for visualization of tree and annotation data

DOI: 10.18129/B9.bioc.ggtree

Bioconductor version: Release (3.22)

'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] ORCID: 0000-0002-6485-8781, Tommy Tsan-Yuk Lam [aut, ths], Shuangbin Xu [aut] ORCID: 0000-0003-3513-5362, 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 (from within R, entercitation("ggtree")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("ggtree")

For older versions of R, please refer to the appropriateBioconductor 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	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment,Annotation,Clustering,DataImport,MultipleSequenceAlignment,Phylogenetics,ReproducibleResearch,Software,Visualization
Version	4.0.1
In Bioconductor since	BioC 3.1 (R-3.2) (10.5 years)
License	Artistic-2.0
Depends	R (>= 4.2.0)
Imports	ape,aplot,dplyr,ggplot2 (>= 4.0.0), grid,magrittr, methods,purrr,rlang,ggfun (>= 0.1.7),yulab.utils (>= 0.1.6),tidyr,tidytree (>= 0.4.5),treeio(>= 1.8.0), utils,scales, stats,cli,ggiraph (>= 0.9.1)
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

Suggests	emojifont,ggimage,ggplotify,shadowtext, grDevices,knitr,prettydoc,rmarkdown,testthat,tibble,glue,Biostrings
Linking To
Enhances
Depends On Me	ggtreeDendro,tanggle
Imports Me	cardelino,cellmig,cogeqc,crumblr,DspikeIn,enrichplot,ggmsa,ggtreeExtra,ggtreeSpace,iSEEtree,lefser,LymphoSeq,MetaboDynamics,miaViz,MicrobiotaProcess,mitology,orthogene,philr,scBubbletree,scDotPlot,singleCellTK,sitePath,SVP,systemPipeTools,treeclimbR,treekoR,BioVizSeq,DAISIEprep,ddtlcm,delimtools,dowser,EvoPhylo,FossilSim,genBaRcode,harrietr,mycolorsTB,numbat,Platypus,RevGadgets,scistreer,shinyTempSignal,STraTUS,Sysrecon,TransProR
Suggests Me	compcodeR,fastreeR,syntenet,TreeAndLeaf,treeio,TreeSummarizedExperiment,universalmotif,aplot,aplotExtra,CoOL,DAISIE,deeptime,gggenomes,ggimage,ggtangle,idiogramFISH,MetaNet,nosoi,oppr,PCMBase,pctax,RAINBOWR,rhierbaps,rphylopic,treestructure
Links To Me
Build Report	Build Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source Package	ggtree_4.0.1.tar.gz
Windows Binary (x86_64)	ggtree_4.0.1.zip
macOS Binary (x86_64)	ggtree_4.0.1.tgz
macOS Binary (arm64)	ggtree_4.0.1.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 3.22	Source Archive

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