#' @title Pseudo-time ordering

#' @description This function takes the exact output of exprmclust function and

#'   construct Pseudo-time ordering by mapping all cells onto the path that

#'   connects cluster centers.

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

#' @param quiet if `TRUE`, suppresses intermediary output

#' @param export if `TRUE`, exports order table to csv

#' @param filename Name of the exported file (if `export=TRUE`)

#' @importFrom TSCAN TSCANorder

#' @return The DISCBIO-class object input with the kordering slot filled.

setGeneric("pseudoTimeOrdering", function(

    object,

    quiet = FALSE,

    export = FALSE,

    filename = "Cellular_pseudo-time_ordering") {

  standardGeneric("pseudoTimeOrdering")

})

#' @export

#' @rdname pseudoTimeOrdering

setMethod(

  "pseudoTimeOrdering",

  signature = "DISCBIO",

  definition = function(object, quiet, export, filename) {

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

    # Validating

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

    ran_k <- length(object@kmeans$kpart) > 0

    ran_m <- length(object@MBclusters) > 0

    if (ran_k) {

      Obj <- object@fdata

      Names <- object@cpart

      lpsmclust <- Exprmclust(Obj, K = 4, reduce = FALSE, cluster = Names)

      lpsorder <- TSCANorder(lpsmclust)

    } else if (ran_m) {

      Obj <- object@fdata

      Names <- names(object@MBclusters$clusterid)

      lpsmclust <- object@MBclusters

      lpsorder <- TSCANorder(lpsmclust)

    } else {

      stop("run clustexp before this pseudoTimeOrdering")

    }

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

    # Ordering

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

    sampleNames <- colnames(Obj)

    orderID <- lpsorder

    order <- seq_len(length(lpsorder))

    orderTable <- data.frame(order, orderID)

    if (export) write.csv(orderTable, file = paste0(filename, ".csv"))

    if (!quiet) print(orderTable)

    FinalOrder <- orderTable[match(sampleNames, orderTable$orderID), ]

    out_order <- FinalOrder[, 1]

    names(out_order) <- names(Names)

    if (ran_k) {

      object@kordering <- out_order

    } else if (ran_m) {

      object@MBordering <- out_order

    }

    return(object)

  }

)