R/plotSlice.R

In ChemoSpec2D: Exploratory Chemometrics for 2D Spectroscopy

#'
#' Plot a Slice of a Spectra2D Object
#'
#' Plots a slice of a 2D spectrum stored in a \code{\link{Spectra2D}} object.
#'
#' @param spectra An object of S3 class \code{\link{Spectra2D}}.
#'
#' @param which A single integer specifying which 2D spectrum from which to
#'   plot the slice.
#'
#' @param F2 A single frequency to plot.  Matched to the nearest value.
#'
#' @param F1 As for \code{F2}.
#'
#' @param showGrid Logical. If TRUE, show a dotted gray line at each x axis tick mark.
#'
#' @param \ldots Additional parameters to be passed to the plotting routines.
#'
#' @section Note:
#' Only one of \code{F2} or \code{F1} should be given.
#'
#' @return Side effect is a plot.
#'
#' @author Bryan A. Hanson, DePauw University.
#'
#' @keywords hplot
#'
#' @export
#'
#' @examples
#'
#' data(MUD1)
#' plotSlice(MUD1, F1 = 22, main = "Slice @ F1 = 22 ppm")
plotSlice <- function(spectra, which = 1, F2 = NULL, F1 = NULL, showGrid = TRUE, ...) {
  .chkArgs(mode = 21L)
  chkSpectra(spectra)

  if ((!is.null(F2)) & (!is.null(F1))) stop("Only one of F2 or F1 may be given")

  if (!is.null(F2)) {
    if (length(F2) != 1L) stop("F2 must be a single value")
    msg <- "F2 is out of range"
    if (F2 > max(spectra$F2)) stop(msg)
    if (F2 < min(spectra$F2)) stop(msg)
    F2i <- findInterval(F2, spectra$F2)
    F2i <- length(spectra$F2) - F2i + 1
    plot(spectra$F1, spectra$data[[which]][, F2i],
      type = "l",
      xlab = spectra$unit[2], ylab = "intensity (entire data set)", ...
    )
    if (showGrid) abline(v = axTicks(1), col = "gray", lty = "dotted")
  }

  if (!is.null(F1)) {
    if (length(F1) != 1L) stop("F1 must be a single value")
    msg <- "F1 is out of range"
    if (F1 > max(spectra$F1)) stop(msg)
    if (F1 < min(spectra$F1)) stop(msg)
    F1i <- findInterval(F1, spectra$F1)
    plot(spectra$F2, spectra$data[[which]][F1i, ],
      type = "l",
      xlab = spectra$unit[1], ylab = "intensity (entire data set)", ...
    )
    if (showGrid) abline(v = axTicks(1), col = "gray", lty = "dotted")
  }
}