R/heatmap.test.pos.R

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

heatmap.test.pos <- function(testData, Delta_pos, trainingLabel, testLabel=NULL, Delta_cutoff = 0.95, coef_test, geneList = NULL){
  
  if (is.null(geneList)){
    nPath <- length(trainingLabel) - 1
    pathName <- names(trainingLabel)[-1]
  } else {
    nPath <- length(geneList)
    pathName <- names(geneList)
  }
  
  diffGeneList <- vector("list")
  for (i in 1:nPath){
    diffGeneList[[i]] <- row.names(testData)[Delta_pos[,i] >= Delta_cutoff] ##the cutoff canbe modified
  }
  if (!is.null(testLabel)){
    cc <- as.numeric(as.factor(testLabel))
  } 
  pdf("signature_heatmap_testset_posterior.pdf")
  for (i in 1:nPath){
    tmp <- match(diffGeneList[[i]], row.names(testData))
    path <- testData[tmp, ]
    if (!is.null(testLabel)){
      heatmap(as.matrix(path[,order(coef_test[,i])]),Colv=NA,scale="row",ColSideColors=as.character(cc[order(coef_test[,i])]), col=bluered(128), margins = c(10,10), main=paste(pathName[i],"signature",sep=" "))
    } else {
      heatmap(as.matrix(path[,order(coef_test[,i])]),Colv=NA,scale="row",col=bluered(128), margins = c(10,10), main=paste(pathName[i],"signature",sep=" "))
    }
  }
  invisible(dev.off())
}