R/plotScores.Spectra.R

In ChemoSpecUtils: Functions Supporting Packages ChemoSpec and ChemoSpec2D

#'
#' plotScores.Spectra
#'
#' @author `r .writeDoc_Authors("BH")`
#' @export
#' @noRd
#'
plotScores.Spectra <- function(spectra, so,
                               pcs = c(1, 2), ellipse = "none", tol = "none",
                               use.sym = FALSE, leg.loc = "topright", ...) {

  # This function will handle score plots from classical or robust analyses

  .chkArgs(mode = 12L)
  chkSpectra(spectra)
  if (length(pcs) != 2L) stop("Please supply two scores to plot (argument pcs)")

  variance <- .getVarExplained(so)

  # See stackoverflow.com/a/46289614/633251 for the concepts re: argument handling
  # Use a sensible xlab and ylab if none provided
  args <- as.list(match.call()[-1])
  if (!("xlab" %in% names(args))) {
    xlab <- paste("PC", pcs[1], " score (", format(variance[ pcs[1] ], digits = 2), "%", ")", sep = "")
    args <- c(args, list(xlab = xlab))
  }
  if (!("ylab" %in% names(args))) {
    ylab <- paste("PC", pcs[2], " score (", format(variance[ pcs[2] ], digits = 2), "%", ")", sep = "")
    args <- c(args, list(ylab = ylab))
  }

  # Update & clean the argument list

  do.call(.scorePlot, args)
}