puma (version 3.12.0)

plot-methods: Plot method for pumaPCARes objects

Description

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

Usage

"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)