miaViz

Microbiome Analysis Plotting and Visualization

The scope of this package is the plotting and visualization of microbiome data. The main classes for interfacing is the TreeSummarizedExperiment class.

Using the package

Online tutorials and examples are available at:

• Package homepage
• Orchestrating microbiome analysis with R/Bioconductor online book

Contribution

Feel free to contribute by forking and opening a pull request. Please make sure that required data wrangling should be designed as reusable as possible and potentially find a better home in the mia package.

Additionally, please make sure that working examples are included and that vignetted make use of added functions in either miaViz or the TreeSummarizedExperiment package.

Technical aspects

Let’s use a git flow kind of approach. Development version should be done against the master branch and then merged to release for release. (https://guides.github.com/introduction/flow/)

Installation

Bioc-release

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

BiocManager::install("miaViz")

Bioc-devel

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("miaViz")

Code of conduct

Please note that the miaViz project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.