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
library(puma)
data(affybatch.example)
pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
, "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
eset_mmgmos <- mmgmos(affybatch.example)
pumapca_mmgmos <- pumaPCA(eset_mmgmos)
plot(pumapca_mmgmos)
[Package
puma version 1.2.1
Index]