R/box.plot.test.R

In wevanjohnson/ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

box.plot.test <- function(coef_test, trainingLabel, testLabel, geneList=NULL){
  if (is.null(geneList)){
    nPath <- length(trainingLabel) - 1
    pathName <- names(trainingLabel)[-1]
  } else {
    nPath <- length(geneList)
    pathName <- names(geneList)
  }
  
  pdf("pathway_activity_boxplot_testset.pdf")
  for(i in 1:nPath){
    boxplot(coef_test[,i] ~ as.factor(testLabel), main=paste("box-plot of", pathName[i], "pathway activity in test samples",sep=" "))
    points(jitter(as.numeric(as.factor(testLabel)),amount=0.2), coef_test[,i], pch=17, col=4)
  }
  invisible(dev.off())
}