ggtreeExtra

This is the released version of ggtreeExtra; for the devel version, see ggtreeExtra.

An R Package To Add Geometric Layers On Circular Or Other Layout Tree Of "ggtree"

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DOI: 10.18129/B9.bioc.ggtreeExtra

Bioconductor version: Release (3.22)

'ggtreeExtra' extends the method for mapping and visualizing associated data on phylogenetic tree using 'ggtree'. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by 'ggtree' with the grammar of 'ggplot2'.

Author: Shuangbin Xu [aut, cre] ORCID iD ORCID: 0000-0003-3513-5362 , Guangchuang Yu [aut, ctb] ORCID iD ORCID: 0000-0002-6485-8781

Maintainer: Shuangbin Xu <xshuangbin at 163.com>

Citation (from within R, enter citation("ggtreeExtra")):

Installation

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


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

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("ggtreeExtra")

ggtreeExtra HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Annotation, Phylogenetics, Software, Visualization

Version 1.20.0

In Bioconductor since BioC 3.12 (R-4.0) (5 years)

License GPL (>= 3)

Depends

Imports ggplot2 (>= 4.0.0), utils, rlang, ggnewscale, stats, ggtree, tidytree (>= 0.3.9), cli, magrittr

System Requirements

URL https://github.com/YuLab-SMU/ggtreeExtra/

Bug Reports https://github.com/YuLab-SMU/ggtreeExtra/issues

Suggests treeio, ggstar, patchwork, knitr, rmarkdown, prettydoc, markdown, testthat (>= 3.0.0), pillar

Linking To

Enhances

Depends On Me

Imports Me DspikeIn, MicrobiotaProcess

Suggests Me enrichplot, ggmsa, pctax, TransProR

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package ggtreeExtra_1.20.0.tar.gz

Windows Binary (x86_64) ggtreeExtra_1.19.0.zip

macOS Binary (x86_64) ggtreeExtra_1.20.0.tgz

macOS Binary (arm64) ggtreeExtra_1.20.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/ggtreeExtra

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ggtreeExtra

Bioc Package Browser https://code.bioconductor.org/browse/ggtreeExtra/

Package Short Url https://bioconductor.org/packages/ggtreeExtra/

Package Downloads Report Download Stats

Old Source Packages for BioC 3.22 Source Archive