R/DIscBIO-generic-plotGap.R

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

#' @title Plotting Gap Statistics
#' @export
#' @rdname plotGap
#' @param object \code{DISCBIO} class object.
#' @param y_limits 2-length numeric vector with the limits for the gap plot
#' @return A plot of the gap statistics
setGeneric(
  "plotGap", function(object, y_limits = NULL) standardGeneric("plotGap")
)

#' @rdname plotGap
setMethod(
  f = "plotGap",
  signature = "DISCBIO",
  definition = function(object, y_limits) {
    if (length(object@kmeans$kpart) == 0) {
      stop("run clustexp before plotgap")
    }
    gap <- object@kmeans$gap
    if (is.null(y_limits)) {
      y_lo <- min(gap$Tab[, "gap"]) - 1 * max(gap$Tab[, "SE.sim"])
      y_up <- max(gap$Tab[, "gap"]) + 1 * max(gap$Tab[, "SE.sim"])
      y_limits <- c(y_lo, y_up)
    }
    plot(
      gap,
      las = 1, ylim = y_limits, main = "Gap Statistics"
    )
  }
)