R/heatmap.train.R

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

heatmap.train <- function(diffGeneList, trainingData, trainingLabel, outPath) {
  nPath <- length(trainingLabel) - 1

  bgPosB <- NULL; edPosB <- NULL
  for (i in seq_len(length(trainingLabel[[1]]))) {
    bgPosB <- c(bgPosB, trainingLabel[[1]][[i]][1])
    edPosB <- c(edPosB,
                trainingLabel[[1]][[i]][length(trainingLabel[[1]][[i]])])
  }
  bgPosS <- NULL; edPosS <- NULL
  for (i in 2:length(trainingLabel)) {
    bgPosS <- c(bgPosS, trainingLabel[[i]][1])
    edPosS <- c(edPosS, trainingLabel[[i]][length(trainingLabel[[i]])])
  }

  grDevices::pdf(outPath)
  for (i in 1:nPath) {
    tmp <- match(diffGeneList[[i]], row.names(trainingData))
    path <- trainingData[tmp, ]
    sig <- rowMeans(path[, bgPosS[i]:edPosS[i]]) - rowMeans(path[, bgPosB[i]:edPosB[i]])
    ord <- order(sig)
    path_ord <- path[ord, c(bgPosB[i]:edPosB[i], bgPosS[i]:edPosS[i])]
    cc <- rep(c(1, 2), c((edPosB[i] - bgPosB[i] + 1),
                         (edPosS[i] - bgPosS[i] + 1)))
    stats::heatmap(as.matrix(path_ord), scale = "row", Rowv = NA, Colv = NA,
                   ColSideColors = as.character(cc), col = gplots::bluered(128),
                   margins = c(10, 10),
                   main = paste(names(trainingLabel)[i + 1],
                                "signature", sep = " "))
  }
  invisible(grDevices::dev.off())
}