--- a
+++ b/R/DIscBIO-generic-plotExptSNE.R
@@ -0,0 +1,102 @@
+#' @title Highlighting gene expression in the t-SNE map
+#' @description The t-SNE map representation can also be used to analyze
+#'   expression of a gene or a group of genes, to investigate cluster specific
+#'   gene expression patterns
+#' @param object \code{DISCBIO} class object.
+#' @param g  Individual gene name or vector with a group of gene names
+#'   corresponding to a subset of valid row names of the \code{ndata} slot of
+#'   the \code{DISCBIO} object.
+#' @param n String of characters representing the title of the plot. Default is
+#'   NULL and the first element of \code{g} is chosen.
+#' @return t-SNE plot for one particular gene
+
+setGeneric("plotExptSNE", function(object, g, n = NULL) {
+  standardGeneric("plotExptSNE")
+})
+
+#' @export
+#' @rdname plotExptSNE
+setMethod(
+  "plotExptSNE",
+  signature = "DISCBIO",
+  definition = function(object, g, n = NULL) {
+    # ======================================================================
+    # Validation
+    # ======================================================================
+    ran_k <- length(object@tsne) > 0
+    ran_m <- length(object@MBtsne) > 0
+    if (ran_k) {
+      x <- object@tsne
+    } else if (ran_m) {
+      x <- object@MBtsne
+    } else {
+      stop("run comptSNE before plotExptSNE")
+    }
+    if (length(intersect(g, rownames(object@ndata))) < length(unique(g))) {
+      stop(
+        "second argument does not correspond to set of rownames slot",
+        "ndata of SCseq object"
+      )
+    }
+    if (is.null(n)) n <- g[1]
+    # ======================================================================
+    # Plotting
+    # ======================================================================
+    logObj <- log(object@ndata)
+    l <- apply(logObj[g, ] - .1, 2, sum) + .1
+    mi <- min(l, na.rm = TRUE)
+    ma <- max(l, na.rm = TRUE)
+    ColorRamp <- colorRampPalette(
+      rev(brewer.pal(n = 7, name = "RdYlBu"))
+    )(100)
+    ColorLevels <- seq(mi, ma, length = length(ColorRamp))
+    v <- round((l - mi) / (ma - mi) * 99 + 1, 0)
+    layout(
+      matrix(
+        data = c(1, 3, 2, 4),
+        nrow = 2,
+        ncol = 2
+      ),
+      widths = c(5, 1, 5, 1),
+      heights = c(5, 1, 1, 1)
+    )
+    opar <- withr::local_par(mar = c(3, 5, 2.5, 2))
+    on.exit(withr::local_par(opar))
+    plot(
+      x,
+      xlab = "Dim 1",
+      ylab = "Dim 2",
+      main = n,
+      pch = 20,
+      cex = 0,
+      col = "grey",
+      las = 1
+    )
+    for (k in seq_len(length(v))) {
+      points(
+        x[k, 1],
+        x[k, 2],
+        col = ColorRamp[v[k]],
+        pch = 20,
+        cex = 1.5
+      )
+    }
+    opar <- withr::local_par(mar = c(3, 2.5, 2.5, 2))
+    on.exit(withr::local_par(opar))
+    image(
+      1,
+      ColorLevels,
+      matrix(
+        data = ColorLevels,
+        ncol = length(ColorLevels),
+        nrow = 1
+      ),
+      col = ColorRamp,
+      xlab = "",
+      ylab = "",
+      las = 1,
+      xaxt = "n"
+    )
+    layout(1)
+  }
+)