miaViz

DOI: 10.18129/B9.bioc.miaViz    

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

Microbiome Analysis Plotting and Visualization

Bioconductor version: Development (3.17)

The miaViz package implements plotting function to work with TreeSummarizedExperiment and related objects in a context of microbiome analysis. Among others this includes plotting tree, graph and microbiome series data. The package is part of the broader miaverse framework.

Author: Felix G.M. Ernst [aut] , Tuomas Borman [aut, cre] , Leo Lahti [aut]

Maintainer: Tuomas Borman <tuomas.v.borman at utu.fi>

Installation

To install this package, start R (version "4.3") and enter:

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

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

BiocManager::install("miaViz")

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("miaViz")

 

HTML	R Script	miaViz
PDF		Reference Manual

Details

biocViews	Microbiome, Software, Visualization
Version	1.7.0
In Bioconductor since	BioC 3.13 (R-4.1) (1.5 years)
License	Artistic-2.0 | file LICENSE
Depends	R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia(>= 0.99), ggplot2, ggraph (>= 2.0)
Imports	methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, testthat, patchwork, microbiomeDataSets
SystemRequirements
Enhances
URL
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	miaViz_1.7.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/miaViz
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/miaViz
Package Short Url	https://bioconductor.org/packages/miaViz/
Package Downloads Report	Download Stats