plot-methods: Plot method for pumaPCARes objects

In puma: Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)

Description

This is the method to plot objects of class pumaPCARes. It will produce a scatter plot of two of the principal components

Usage

## S4 method for signature 'pumaPCARes,missing'
plot(..., firstComponent = 1, secondComponent = 2, useFilenames = FALSE, phenotype = pData(pumaPCARes@phenoData), legend1pos = "topright", legend2pos = "bottomright")

Arguments

...	Optional graphical parameters to adjust different components of the plot
firstComponent	Integer identifying which principal component to plot on the x-axis
secondComponent	Integer identifying which principal component to plot on the x-axis
useFilenames	Boolean. If TRUE then use filenames as plot points. Otherwise just use points.
phenotype	Phenotype information
legend1pos	String indicating where to put legend for first factor
legend2pos	String indicating where to put legend for second factor

Examples

	#	Next 4 lines commented out to save time in package checks, and saved version used
    # if (require(affydata)) {
	#	data(Dilution)
	#	eset_mmgmos <- mmgmos(Dilution)
	# }
	data(eset_mmgmos)
	pumapca_mmgmos <- pumaPCA(eset_mmgmos)
	plot(pumapca_mmgmos)

puma documentation built on Nov. 8, 2020, 11:08 p.m.