miaViz

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

Microbiome Analysis Plotting and Visualization


Bioconductor version: Development (3.20)

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] , Théotime Pralas [ctb], Nitesh Turaga [ctb], Chouaib Benchraka [ctb], Sam Hillman [ctb], Muluh Muluh [ctb], Noah De Gunst [ctb], Ely Seraidarian [ctb], Himmi Lindgren [ctb], Vivian Ikeh [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 "4.4") 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")
miaViz HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Microbiome, Software, Visualization
Version 1.13.14
In Bioconductor since BioC 3.13 (R-4.1) (3.5 years)
License Artistic-2.0 | file LICENSE
Depends R (>= 4.0), SummarizedExperiment, TreeSummarizedExperiment, mia(>= 1.13.0), ggplot2, ggraph (>= 2.0)
Imports methods, stats, S4Vectors, BiocGenerics, BiocParallel, DelayedArray, scater, ggtree, ggnewscale, viridis, tibble, tidytext, tidytree, tidygraph, rlang, purrr, tidyr, dplyr, ape, DirichletMultinomial, ggrepel, SingleCellExperiment
System Requirements
URL
See More
Suggests knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, bluster, ComplexHeatmap, circlize
Linking To
Enhances
Depends On Me
Imports Me iSEEtree
Suggests Me MGnifyR, mia, miaSim
Links To Me
Build Report Build Report

Package Archives

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

Source Package miaViz_1.13.14.tar.gz
Windows Binary miaViz_1.13.14.zip
macOS Binary (x86_64) miaViz_1.13.14.tgz
macOS Binary (arm64) miaViz_1.13.14.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/
Package Downloads Report Download Stats