plot-methods {puma} | R Documentation |
This is the method to plot objects of class pumaPCARes. It will produce a scatter plot of two of the principal components
## S4 method for signature 'pumaPCARes,missing' plot(..., firstComponent = 1, secondComponent = 2, useFilenames = FALSE, phenotype = pData(pumaPCARes@phenoData), legend1pos = "topright", legend2pos = "bottomright")
... |
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 |
# 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)