#' @title Plot PCA symbols

#' @description Generates a plot of grouped PCA components

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

#' @param types If types=NULL then the names of the cells will be grouped

#'   automatically. Default is NULL

#' @importFrom grDevices rainbow

#' @importFrom graphics legend

#' @return Plot of the Principal Components

#'

setGeneric("PCAplotSymbols", function(object, types = NULL) {

  standardGeneric("PCAplotSymbols")

})

#' @export

#' @rdname PCAplotSymbols

setMethod(

  "PCAplotSymbols",

  signature = "DISCBIO",

  definition = function(object, types = NULL) {

    if (length(object@MBclusters) == 0) {

      stop("run Exprmclust before PCAplotSymbols")

    }

    total <- object@MBclusters

    types <- names(object@fdata)

    types <- gsub("_[0-9]+", "", types)

    coloc <- rainbow(length(unique(types)))

    total <- object@MBclusters$pcareduceres

    syms <- vector()

    plot(

      total[, 1],

      total[, 2],

      xlab = "PC1",

      ylab = "PC2",

      pch = 20,

      cex = 0,

      col = "grey",

      las = 1

    )

    for (i in seq_len(length(unique(types)))) {

      f <- types == sort(unique(types))[i]

      syms <- append(syms, ((i - 1) %% 25) + 1)

      points(

        total[f, 1],

        total[f, 2],

        col = coloc[i],

        pch = ((i - 1) %% 25) + 1,

        cex = 1

      )

    }

    legend(

      "topright",

      legend = sort(unique(types)),

      col = coloc,

      pch = syms

    )

  }

)