https://github.com/microbiome/miaviz

Microbiome Analysis Plotting and Visualization
https://github.com/microbiome/miaviz

bioconductor microbiome microbiome-analysis plotting visualization

Last synced: 6 months ago
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Microbiome Analysis Plotting and Visualization

• Host: GitHub
• URL: https://github.com/microbiome/miaviz
• Owner: microbiome
• License: artistic-2.0
• Created: 2020-11-03T10:50:30.000Z (over 5 years ago)
• Default Branch: devel
• Last Pushed: 2025-05-10T14:41:13.000Z (10 months ago)
• Last Synced: 2025-05-10T15:26:33.104Z (10 months ago)
• Topics: bioconductor, microbiome, microbiome-analysis, plotting, visualization
• Language: R
• Homepage: https://microbiome.github.io/miaViz
• Size: 1.46 GB
• Stars: 11
• Watchers: 8
• Forks: 12
• Open Issues: 6
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS
  • Contributing: CONTRIBUTING.md
  • License: LICENSE

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README

          
# miaViz 

[![Platforms](http://bioconductor.org/shields/availability/release/miaViz.svg)](https://bioconductor.org/packages/release/bioc/html/miaViz.html)

[![rworkflows](https://github.com/microbiome/miaViz/actions/workflows/rworkflows.yml/badge.svg?branch=devel)](https://github.com/microbiome/miaViz/actions)

[![Bioc-release](http://bioconductor.org/shields/build/release/bioc/miaViz.svg)](http://bioconductor.org/packages/release/bioc/html/miaViz.html)

[![Bioc-age](http://bioconductor.org/shields/years-in-bioc/miaViz.svg)](https://bioconductor.org/packages/release/bioc/html/miaViz.html)

[![Codecov test

coverage](https://codecov.io/gh/microbiome/miaViz/branch/devel/graph/badge.svg)](https://codecov.io/gh/microbiome/miaViz?branch=devel)

[![Dependencies](http://bioconductor.org//shields/dependencies/release/miaViz.svg)](https://bioconductor.org/packages/release/bioc/html/miaViz.html)

## 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](https://microbiome.github.io/miaViz/) 

- [Orchestrating microbiome analysis with R/Bioconductor online book](https://microbiome.github.io/OMA)

## 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`](https://github.com/FelixErnst/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`](https://github.com/fionarhuang/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](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html).

By contributing to this project, you agree to abide by its terms.