#' @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)

  }

)