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.Rbuildignore (83, 2023-09-11)
DESCRIPTION (1854, 2023-09-11)
LICENSE (9073, 2023-09-11)
NAMESPACE (4008, 2023-09-11)
NEWS (685, 2023-09-11)
R (0, 2023-09-11)
R\miaViz.R (1638, 2023-09-11)
R\plotAbundance.R (22568, 2023-09-11)
R\plotAbundanceDensity.R (17111, 2023-09-11)
R\plotCCA.R (25120, 2023-09-11)
R\plotColTile.R (6914, 2023-09-11)
R\plotDMN.R (2328, 2023-09-11)
R\plotGraph.R (26053, 2023-09-11)
R\plotPrevalence.R (22449, 2023-09-11)
R\plotSeries.R (13155, 2023-09-11)
R\plotTree.R (59685, 2023-09-11)
R\treeData.R (9017, 2023-09-11)
R\utils.R (1965, 2023-09-11)
R\utils_plotting.R (17289, 2023-09-11)
data (0, 2023-09-11)
data\col_graph.rda (1160, 2023-09-11)
data\row_graph.rda (23109, 2023-09-11)
data\row_graph_order.rda (3347, 2023-09-11)
man (0, 2023-09-11)
man\figures (0, 2023-09-11)
man\figures\mia_logo.png (63143, 2023-09-11)
man\mia-datasets.Rd (1363, 2023-09-11)
man\mia-plot-args.Rd (6067, 2023-09-11)
man\miaViz-package.Rd (433, 2023-09-11)
man\plotAbundance.Rd (5793, 2023-09-11)
man\plotAbundanceDensity.Rd (6173, 2023-09-11)
man\plotCCA.Rd (6216, 2023-09-11)
man\plotColTile.Rd (1668, 2023-09-11)
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# miaViz [](https://github.com/microbiome/miaViz/actions) [](https://github.com/microbiome/mia/actions/workflows/check-bioc.yml) [](http://bioconductor.org/packages/release/bioc/html/miaViz.html) [](https://codecov.io/gh/microbiome/miaViz?branch=master) ## 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.

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