#' @title Plotting the pseudo-time ordering in the t-SNE map

#' @description The tSNE representation can also be used to show the pseudo-time

#'   ordering.

#' @param object \code{DISCBIO} class object.

#' @return A plot of the pseudo-time ordering.

setGeneric("plotOrderTsne", function(object) {

  standardGeneric("plotOrderTsne")

})

#' @export

#' @rdname plotOrderTsne

setMethod(

  "plotOrderTsne",

  signature = "DISCBIO",

  definition = function(object) {

    ran_k <- length(object@tsne) > 0

    ran_m <- length(object@MBtsne) > 0

    if (ran_k) {

      total <- rbind(object@ndata, object@kordering)

      clustering_method <- "k-means"

      x <- object@tsne

    } else if (ran_m) {

      total <- rbind(object@ndata, object@MBordering)

      clustering_method <- "model-based"

      x <- object@MBtsne

    } else {

      stop("run comptsne before plotOrderTsne")

    }

    rownames(total)[nrow(total)] <- paste(

      "Pseudo-time ordering of", clustering_method, "clustering"

    )

    g <- rownames(total)[nrow(total)]

    n <- g[1]

    l <- apply(total[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)

  }

)