plotDMN: Plotting Dirichlet-Multinomial Mixture Model data

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

Plotting Dirichlet-Multinomial Mixture Model data

Description

To plot DMN fits generated with mia use plotDMNFit.

Usage

plotDMNFit(x, name = "DMN", type = c("laplace", "AIC", "BIC"), ...)

## S4 method for signature 'SummarizedExperiment'
plotDMNFit(x, name = "DMN", type = c("laplace", "AIC", "BIC"))

Arguments

x	a SummarizedExperiment object contain the DMN data in metadata.
name	the name to store the result in metadata
type	the type of measure for access the goodness of fit. One of ‘laplace’, ‘AIC’ or ‘BIC’.
...	optional arguments not used.

Value

plotDMNFit returns a ggplot2 plot.

See Also

calculateDMN

Examples

library(mia)
library(bluster)

# Get dataset
data("peerj13075", package = "mia")
tse <- peerj13075

# Cluster the samples
tse <- cluster(tse, DmmParam(k = 1:4), name = "DMM", full = TRUE)

# Plot the fit
plotDMNFit(tse, name = "DMM", type = "laplace")

microbiome/miaViz documentation built on April 21, 2024, 8:45 a.m.