R/heatmap.test.prior.R

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

heatmap.test.prior <- function(diffGeneList, testData, trainingLabel,
                               testLabel=NULL, coef_test, geneList=NULL, outPath) {
  if (is.null(geneList)) {
    nPath <- length(trainingLabel) - 1
    pathName <- names(trainingLabel)[-1]
  } else {
    nPath <- length(geneList)
    pathName <- names(geneList)
  }

  grDevices::pdf(outPath)
  if (!is.null(testLabel)) {
    cc <- as.numeric(as.factor(testLabel))
  }
  for (i in 1:nPath) {
    tmp <- match(diffGeneList[[i]], row.names(testData))
    path <- testData[tmp, ]
    if (!is.null(testLabel)) {
      stats::heatmap(as.matrix(path[, order(coef_test[, i])]), Colv = NA,
                     scale = "row",
                     ColSideColors = as.character(cc[order(coef_test[, i])]),
                     col = gplots::bluered(128), margins = c(10, 10),
                     main = paste(pathName[i], "signature", sep = " "))
    } else {
      stats::heatmap(as.matrix(path[, order(coef_test[, i])]), Colv = NA,
                     scale = "row", col = gplots::bluered(128),
                     margins = c(10, 10), main = paste(pathName[i],
                                                       "signature", sep = " "))
    }
  }
  invisible(grDevices::dev.off())
}