R/plotmat.R

In hyperSpec: Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)

##' Plot spectra matrix
##'
##' plots the spectra matrix.
##'
##' If package plotrix is available, a color legend is plotted to the right. The right margin is set
##' to at least 5 lines.
##' @param object hyperSpec object
##' @param y character giving the name of the extra data column to label the y axis.
##' @param ylab y axis label, defaults to \code{"row"} and the label of the extra data column used
##' for the y axis, respectively.
##' @param col see  \code{\link[graphics]{image}}
##' @param ... further parameters for \code{\link[graphics]{image}}
##' @param contour should \code{\link[graphics]{contour}} be called instead of
##' \code{\link[graphics]{image}}?
##' @author Claudia Beleites
##' @seealso  \code{\link[graphics]{image}}, \code{\link[graphics]{contour}}, \code{\link[hyperSpec]{levelplot}}
##' @export 
##' @examples
##' plotmat (laser, col = alois.palette (100))
##' 
##' plot (laser, "mat")
##'
##' plotmat (laser)
##' plotmat (laser, contour = TRUE, add = TRUE)
##'
##' ## use different y axis labels
##'
##' plotmat (laser, "t")
##' 
##' plotmat (laser, laser$t / 3600, ylab = "t / h")
plotmat <- function (object, y = ".row", ylab, col = alois.palette (20), ...,
                     contour = FALSE){

  chk.hy (object)
  validObject (object)

  if (is.character (y)) {
    if (missing (ylab))
      ylab <- switch (y,
                      .row = "row",
                      labels (object, y))
        
    y <- switch (y,
                 .row = seq_len (nrow (object)),
                 object@data [[y]])
  }
  
  dots <- modifyList (list (x = wl (object),
                            y = y,
                            z = t (object [[]]),
                            xlab = labels (object, ".wavelength"),
                            ylab = ylab,
                            col = col
                            ),
                      list (...))

  
  if (contour)
    do.call ("contour", dots)
  else {
    ## leave at least 4 lines right margin
    mar <- par()$ mar
    if (mar [4] < 5)
      par (mar = c (mar [1 : 3], 5))
    
    do.call ("image", dots)
    par (mar = mar)

    ## color legend
    if (requireNamespace ("plotrix")){
    
      usr <- par()$usr

      dx <- diff (usr [1 : 2])
    
      plotrix::color.legend (usr [2] + 0.05 * dx,
      											 usr [3],
      											 usr [2] + 0.10 * dx,
      											 usr [4],
      											 pretty (range (object, na.rm = TRUE)),
      											 col,
      											 align="rb",gradient="y")
    } else {
      warning ("package 'plotrix' not available: omitting legend.")
    }

  }

  
}