Microbiome Analysis Plotting and Visualization

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Documentation for package ‘miaViz’ version 1.17.9

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.
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'