R/scatter.plot.test.R

In ASSIGN: Adaptive Signature Selection and InteGratioN (ASSIGN)

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

  if (!is.null(testLabel)) {
    cc <- as.factor(testLabel)
  } else {
    cc <- rep(1, NROW(coef_test))
  }

  grDevices::pdf(outPath)
  for (i in 1:nPath) {
    ord <- order(coef_test[, i])
    cc_ord <- cc[ord]
    graphics::plot(coef_test[ord, i], col = cc_ord, pch = 19, cex = 0.7,
                   xlab = "Test sample", ylab = paste(pathName[i],
                                                      "pathway activity",
                                                      sep = " "),
                   main = paste("Evaluate in vitro", pathName[i],
                                "signature in cancer samples", sep = " "))
    if (!is.null(testLabel)) {
      graphics::legend("topleft", legend = unique(testLabel), col = unique(cc),
                       pch = 19, cex = 0.7)
    }
  }
  invisible(grDevices::dev.off())
}