miaViz

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see miaViz.

Microbiome Analysis Plotting and Visualization

Bioconductor version: 3.18

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

Author: Tuomas Borman [aut, cre] , Felix G.M. Ernst [aut] , Leo Lahti [aut] , Basil Courbayre [ctb], Giulio Benedetti [ctb]

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

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

Installation

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


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

miaViz HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microbiome, Software, Visualization

Version 1.10.0

In Bioconductor since BioC 3.13 (R-4.1) (3 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, ggrepel, SingleCellExperiment

System Requirements

URL

Suggests knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, microbiomeDataSets, bluster

Linking To

Enhances

Depends On Me

Imports Me

Suggests Me miaSim

Links To Me

Build Report Build Report

Package Archives

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

Source Package miaViz_1.10.0.tar.gz

Windows Binary miaViz_1.10.0.zip (64-bit only)

macOS Binary (x86_64) miaViz_1.10.0.tgz

macOS Binary (arm64) miaViz_1.10.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/miaViz

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/miaViz

Bioc Package Browser https://code.bioconductor.org/browse/miaViz/

Package Short Url https://bioconductor.org/packages/miaViz/

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