tanggle
This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see tanggle.
Visualization of Phylogenetic Networks
Bioconductor version: 3.14
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)
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("tanggle")):
Installation
To install this package, start R (version "4.1") 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")| ***tanggle***: Visualization of phylogenetic networks in a *ggplot2* framework | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Clustering, DataImport, MultipleSequenceAlignment, Phylogenetics, Software, Visualization |
| Version | 1.0.0 |
| 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 |
| 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_1.0.0.tar.gz |
| Windows Binary | tanggle_1.0.0.zip |
| macOS 10.13 (High Sierra) | tanggle_1.0.0.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 |
| Old Source Packages for BioC 3.14 | Source Archive |