miaViz

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

Microbiome Analysis Plotting and Visualization

Bioconductor version: Development (3.21)

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: ), Felix G.M. Ernst [aut] (ORCID: ), Leo Lahti [aut] (ORCID: ), Basil Courbayre [ctb], Giulio Benedetti [ctb] (ORCID: ), 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microbiome, Software, Visualization
Version	1.15.0
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

Suggests	knitr, rmarkdown, BiocStyle, testthat, patchwork, vegan, bluster, ComplexHeatmap, circlize
Linking To
Enhances
Depends On Me
Imports Me	iSEEtree
Suggests Me	MGnifyR, miaSim, mia
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	miaViz_1.15.0.tar.gz
Windows Binary (x86_64)
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
Bioc Package Browser	https://code.bioconductor.org/browse/miaViz/
Package Short Url	https://bioconductor.org/packages/miaViz/
Package Downloads Report	Download Stats