miaViz

This is the released version of miaViz; for the devel version, see miaViz.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13

Microbiome Analysis Plotting and Visualization

Bioconductor version: Release (3.23)

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] ORCID: 0000-0002-8563-8884 , Felix G.M. Ernst [aut] ORCID: 0000-0001-5064-0928 , Leo Lahti [aut] ORCID: 0000-0001-5537-637X , Basil Courbayre [ctb], Giulio Benedetti [ctb] ORCID: 0000-0002-8732-7692 , Théotime Pralas [ctb], Chouaib Benchraka [ctb], Sam Hillman [ctb], Geraldson Muluh [ctb], Noah De Gunst [ctb], Ely Seraidarian [ctb], Himmi Lindgren [ctb], Akewak Jeba [ctb] ORCID: 0009-0007-1347-7552 , Vivian Ikeh [ctb]

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

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

Tuomas Borman, Felix G.M. Ernst, Leo Lahti. miaViz: Microbiome Analysis Plotting and Visualization. doi:10.18129/B9.bioc.miaViz, R package version 1.20.0, https://bioconductor.org/packages/miaViz.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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	1.20.0
In Bioconductor since	BioC 3.13 (R-4.1) (5.5 years)
License	Artistic-2.0 \| file LICENSE
Depends	R (>= 4.1.0), ggplot2, ggraph (>= 2.0), mia (>= 1.13.0), SummarizedExperiment, TreeSummarizedExperiment
Imports	ape, BiocGenerics, BiocParallel, DelayedArray, DirichletMultinomial, dplyr, ggnewscale, ggrepel, ggtree, methods, patchwork, rlang, S4Vectors, scales, scater, SingleCellExperiment, stats, tibble, tidygraph, tidyr, tidytext, tidytree, viridis
System Requirements
URL	https://github.com/microbiome/miaViz
Bug Reports	https://github.com/microbiome/miaViz/issues

Suggests	beeswarm, BiocStyle, bluster, circlize, ComplexHeatmap, ggh4x, ggpubr, knitr, maaslin3, mediation, miaTime, patchwork, rmarkdown, rstatix, shadowtext, testthat, vegan, vipor
Linking To
Enhances
Depends On Me
Imports Me	iSEEtree
Suggests Me	HoloFoodR, MGnifyR, mia, miaSim, miaTime, OMA
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	miaViz_1.20.0.tar.gz
Windows Binary (x86_64)	miaViz_1.20.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	miaViz_1.20.0.tgz
macOS Binary (sonoma-arm64)	miaViz_1.20.0.tgz
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