# Microbiome Analysis Plotting and Visualization

## Documentation for package ‘miaViz’ version 1.21.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

miaViz-package | miaViz - Microbiome Analysis Plotting and Visualization
colTreeData | Adding information to tree data in 'TreeSummarizedExperiment'
colTreeData-method | Adding information to tree data in 'TreeSummarizedExperiment'
colTreeData<- | Adding information to tree data in 'TreeSummarizedExperiment'
colTreeData<--method | Adding information to tree data in 'TreeSummarizedExperiment'
col_graph | miaViz example data
combineTreeData | Adding information to tree data in 'TreeSummarizedExperiment'
combineTreeData-method | Adding information to tree data in 'TreeSummarizedExperiment'
deprecate | These functions will be deprecated. Please use other functions instead.
getNeatOrder | Sorting by radial theta angle
getNeatOrder-method | Sorting by radial theta angle
mia-datasets | miaViz example data
mia-plot-args | Additional arguments for plotting
miaViz | miaViz - Microbiome Analysis Plotting and Visualization
plotAbundance | Plotting abundance data
plotAbundance-method | Plotting abundance data
plotAbundanceDensity | Plot abundance density
plotAbundanceDensity-method | Plot abundance density
plotBarplot | Create histogram or barplot of 'assay', 'rowData' or 'colData'
plotBarplot-method | Create histogram or barplot of 'assay', 'rowData' or 'colData'
plotBoxplot | Create boxplot of 'assay', 'rowData' or 'colData'.
plotBoxplot-method | Create boxplot of 'assay', 'rowData' or 'colData'.
plotCCA | Plot RDA or CCA object
plotCCA-method | Plot RDA or CCA object
plotColGraph | Plotting igraph objects with information from a 'SummarizedExperiment'
plotColGraph-method | Plotting igraph objects with information from a 'SummarizedExperiment'
plotColTile | Plot factor data as tiles
plotColTile-method | Plot factor data as tiles
plotColTree | Plotting tree information enriched with information
plotColTree-method | Plotting tree information enriched with information
plotDMN | Plotting Dirichlet-Multinomial Mixture Model data
plotDMNFit | Plotting Dirichlet-Multinomial Mixture Model data
plotDMNFit-method | Plotting Dirichlet-Multinomial Mixture Model data
plotFeaturePrevalence | These functions will be deprecated. Please use other functions instead.
plotFeaturePrevalence-method | These functions will be deprecated. Please use other functions instead.
plotForest | Visualize estimated results with forest plots
plotForest-method | Visualize estimated results with forest plots
plotGraph | Plotting igraph objects with information from a 'SummarizedExperiment'
plotHistogram | Create histogram or barplot of 'assay', 'rowData' or 'colData'
plotHistogram-method | Create histogram or barplot of 'assay', 'rowData' or 'colData'
plotLoadings | Plot feature loadings for TreeSummarizedExperiment objects or feature loadings numeric matrix.
plotLoadings-method | Plot feature loadings for TreeSummarizedExperiment objects or feature loadings numeric matrix.
plotMediation | Visualize mediation
plotMediation-method | Visualize mediation
plotNMDS | Wrapper for scater::plotReducedDim()
plotPrevalence | Plot prevalence information
plotPrevalence-method | Plot prevalence information
plotPrevalentAbundance | Plot prevalence information
plotPrevalentAbundance-method | Plot prevalence information
plotRDA | Plot RDA or CCA object
plotRDA-method | Plot RDA or CCA object
plotRowGraph | Plotting igraph objects with information from a 'SummarizedExperiment'
plotRowGraph-method | Plotting igraph objects with information from a 'SummarizedExperiment'
plotRowPrevalence | Plot prevalence information
plotRowPrevalence-method | Plot prevalence information
plotRowTile | Plot factor data as tiles
plotRowTile-method | Plot factor data as tiles
plotRowTree | Plotting tree information enriched with information
plotRowTree-method | Plotting tree information enriched with information
plotScree | Create a scree plot
plotScree-method | Create a scree plot
plotSeries | Plot Series
plotSeries-method | Plot Series
plotTaxaPrevalence | These functions will be deprecated. Please use other functions instead.
plotTaxaPrevalence-method | These functions will be deprecated. Please use other functions instead.
plotTree | Plotting tree information enriched with information
rowTreeData | Adding information to tree data in 'TreeSummarizedExperiment'
rowTreeData-method | Adding information to tree data in 'TreeSummarizedExperiment'
rowTreeData<- | Adding information to tree data in 'TreeSummarizedExperiment'
rowTreeData<--method | Adding information to tree data in 'TreeSummarizedExperiment'
row_graph | miaViz example data
row_graph_order | miaViz example data
treeData | Adding information to tree data in 'TreeSummarizedExperiment'