tanggle

DOI: 10.18129/B9.bioc.tanggle    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see tanggle.

Visualization of Phylogenetic Networks

Bioconductor version: 3.15

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. 'ggtree' and using functions from 'ape' and 'phangorn'. It extends the 'ggtree' package [@Yu2017] to allow the visualization of phylogenetic networks using the 'ggplot2' syntax. It offers an alternative to the plot functions already available in 'ape' Paradis and Schliep (2019) and 'phangorn' Schliep (2011) .

Author: Klaus Schliep [aut, cre] , Marta Vidal-Garcia [aut], Claudia Solis-Lemus [aut] , Leann Biancani [aut], Eren Ada [aut], L. Francisco Henao Diaz [aut], Guangchuang Yu [ctb]

Maintainer: Klaus Schliep <klaus.schliep at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("tanggle")

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("tanggle")

 

HTML	R Script	***tanggle***: Visualización de redes filogenéticas con *ggplot2*
HTML	R Script	***tanggle***: Visualization of phylogenetic networks in a *ggplot2* framework
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, Software, Visualization
Version	1.2.0
In Bioconductor since	BioC 3.14 (R-4.1) (1 year)
License	Artistic-2.0
Depends	R (>= 4.1), ggplot2 (>= 2.2.0), ggtree
Imports	ape (>= 5.0), phangorn (>= 2.5), utils, methods
LinkingTo
Suggests	tinytest, BiocStyle, ggimage, knitr, rmarkdown
SystemRequirements
Enhances
URL	https://klausvigo.github.io/tanggle https://github.com/KlausVigo/tanggle
BugReports	https://github.com/KlausVigo/tanggle/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	tanggle_1.2.0.tar.gz
Windows Binary	tanggle_1.2.0.zip
macOS Binary (x86_64)	tanggle_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tanggle
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tanggle
Package Short Url	https://bioconductor.org/packages/tanggle/
Package Downloads Report	Download Stats