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tanggle

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

Visualization of Phylogenetic Networks


Bioconductor version: Development (3.19)

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>

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

Installation

To install this package, start R (version "4.4") 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

Details

biocViews Alignment, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, Software, Visualization
Version 1.9.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 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
See More
Suggests tinytest, BiocStyle, ggimage, knitr, rmarkdown
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Package Archives

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

Source Package tanggle_1.9.0.tar.gz
Windows Binary tanggle_1.9.0.zip (64-bit only)
macOS Binary (x86_64) tanggle_1.9.0.tgz
macOS Binary (arm64) tanggle_1.9.0.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