An example usage of this function is as follows:
pData = data.frame(condition=Test.ihc$IHC) rownames(pData) = Test.ihc$PatientID phenoData = new("AnnotatedDataFrame", data=pData) XSet = ExpressionSet(assayData=Test.matrix, phenoData=phenoData) #--Please ensure that the colors are ordered corresponding to the levels in your condition #--For example, my condition levels are Levels: TN Her2+ LA LB1 LB2 so the colors are my.plotPCA(XSet, intgroup=pData$condition, ablne=2.4, colours = c("red", "hotpink", "darkblue", "lightblue", "lightblue3"), LINE.V = T)