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	Character scalar. The name to store the result in metadata (Default: "DMN")
type	Character scalar. 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 <- addCluster(tse, DmmParam(k = 1:4), name = "DMM", full = TRUE)

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

microbiome/miaViz documentation built on Dec. 9, 2024, 2:18 a.m.