#' @title Plotting pseudo-time ordering or gene expression in Model-based

#' clustering in PCA

#' @description The PCA representation can either be used to show pseudo-time

#' ordering or the gene expression of a particular gene.

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

#' @param type either `order` to plot pseudo-time ordering or `exp` to plot gene

#' expression

#' @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. Ignored if `type="order"`.

#' @param n String of characters representing the title of the plot. Default is

#'   NULL and the first element of \code{g} is chosen. Ignored if

#'   `type="order"`.

#' @importFrom RColorBrewer brewer.pal

#' @importFrom grDevices colorRampPalette

#' @importFrom graphics layout par image

#' @return A plot of the PCA.

#' @export

PlotMBpca <- function(object, type = "order", g = NULL, n = NULL) {

  # ==========================================================================

  # Validation

  # ==========================================================================

  data <- object@MBclusters

  if (type == "exp") {

    if (is.null(g)) {

      stop('g must be provided if type="exp"')

    }

    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]

    }

    logObj <- log(object@ndata)

    l <- apply(logObj[g, ] - .1, 2, sum) + .1

    x <- data$pcareduceres

  } else if (type == "order") {

    MBordertable <- cbind(data$pcareduceres, object@MBordering)

    l <- MBordertable[, 3]

    x <- MBordertable

  } else {

    stop("Invalid type. Valid alternatives as 'order' and 'exp'.")

  }

  # ==========================================================================

  # Plotting

  # ==========================================================================

  mi <- min(l, na.rm = TRUE)

  ma <- max(l, na.rm = TRUE)

  ColorRamp <- colorRampPalette(rev(brewer.pal(n = 11, 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(5, 5, 2.5, 2))

  on.exit(withr::local_par(opar))

  plot(

    x[, 1],

    x[, 2],

    xlab = "PC1",

    ylab = "PC2",

    pch = 20,

    cex = 0,

    col = "grey",

    las = 1,

    main = n

  )

  for (k in seq_len(length(v))) {

    points(

      x[k, 1],

      x[k, 2],

      col = ColorRamp[v[k]],

      pch = 20,

      cex = 2

    )

  }

  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 = 2,

    xaxt = "n"

  )

  layout(1)

}