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 1.10.1 Index]