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]