R/heatmap.test.pos.R

In compbiomed/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, outPath) {
  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) {
    ##the cutoff can be modified
    diffGeneList[[i]] <- row.names(testData)[Delta_pos[, i] >= Delta_cutoff]
  }
  if (!is.null(testLabel)) {
    cc <- as.numeric(as.factor(testLabel))
  }
  grDevices::pdf(outPath)
  for (i in 1:nPath) {
    tmp <- match(diffGeneList[[i]], row.names(testData))
    path <- testData[tmp, ]
    #do not print heatmaps if there is 1 or fewer genes in the heatmap
    if (nrow(path) <= 1) {
      next
    }
    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())
}