plot-methods {puma}R Documentation

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

## 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)

[Package puma version 1.8.1 Index]