tanggle

This is the development version of tanggle; for the stable release version, see tanggle.

Visualization of Phylogenetic Networks

Bioconductor version: Development (3.21)

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] (ORCID: ), Marta Vidal-Garcia [aut], Claudia Solis-Lemus [aut] (ORCID: ), Leann Biancani [aut], Eren Ada [aut], L. Francisco Henao Diaz [aut], Guangchuang Yu [ctb]

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

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

Installation

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


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Alignment, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, Software, Visualization
Version	1.13.0
In Bioconductor since	BioC 3.14 (R-4.1) (3 years)
License	Artistic-2.0
Depends	R (>= 4.1), ggplot2 (>= 2.2.0), ggtree
Imports	ape (>= 5.0), phangorn (>= 2.5), utils, methods
System Requirements
URL	https://klausvigo.github.io/tanggle https://github.com/KlausVigo/tanggle
Bug Reports	https://github.com/KlausVigo/tanggle/issues

Suggests	tinytest, BiocStyle, ggimage, knitr, rmarkdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	tanggle_1.13.0.tar.gz
Windows Binary (x86_64)	tanggle_1.13.0.zip (64-bit only)
macOS Binary (x86_64)	tanggle_1.13.0.tgz
macOS Binary (arm64)	tanggle_1.13.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/tanggle
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/tanggle
Bioc Package Browser	https://code.bioconductor.org/browse/tanggle/
Package Short Url	https://bioconductor.org/packages/tanggle/
Package Downloads Report	Download Stats