R/DIscBIO-generic-PCAplotSymbols.R

In DIscBIO: A User-Friendly Pipeline for Biomarker Discovery in Single-Cell Transcriptomics

#' @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
    )
  }
)