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 (3.15)

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 <felix.gm.ernst at outlook.com>, Tuomas Borman <tuomas.v.borman at utu.fi>, Leo Lahti <leo.lahti at iki.fi>

Maintainer: Felix G.M. Ernst <felix.gm.ernst at outlook.com>

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

Installation

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

if (!requireNamespace("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

PDF   Reference Manual

Details

biocViews Microbiome, Software, Visualization
Version 1.3.0
In Bioconductor since BioC 3.13 (R-4.1) (< 6 months)
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
Windows Binary
macOS 10.13 (High Sierra)
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

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