Change of colors in compare.matrix command in r - r

Question

I'm trying to change the colors for the compare.matrix command in r, but the error is always the same:
Error in image.default(x = mids, y = mids, z = mdata, col = c(heat.colors(10)[10:1]), :
formal argument "col" matched by multiple actual arguments
My code is very simple:
compare.matrix(current,ech_b1,nbins=40)
and some of my attempts are:
compare.matrix(current,ech_b1,nbins=40,col=c(grey.colors(5)))
compare.matrix(current,ech_b1,nbins=40,col=c(grey.colors(10)[10:1]))

Answer 1

Assuming you're using compare.matrix() from the SDMTools package, the color arguments appear to be hard-coded into the function, so you'll need to redefine the function in order to make them flexible:
# this shows you the code in the console
SDMTools::compare.matrix
function(x,y,nbins,...){
#---- preceding code snipped ----#
suppressWarnings(image(x=mids, y=mids, z=mdata, col=c(heat.colors(10)[10:1]),...))
#overlay contours
contour(x=mids, y=mids, z=mdata, col="black", lty="solid", add=TRUE,...)
}
So you can make a new one like so, but bummer, there are two functions using the ellipsis that have a col argument predefined. If you'll only be using extra args to image() and not to contour(), this is cheap and easy.
my.compare.matrix <- function(x,y,nbins,...){
#---- preceding code snipped ----#
suppressWarnings(image(x=mids, y=mids, z=mdata,...))
#overlay contours
contour(x=mids, y=mids, z=mdata, col="black", lty="solid", add=TRUE)
}
If, however, you want to use ... for both internal calls, then the only way I know of to avoid confusion about redundant argument names is to do something like:
my.compare.matrix <- function(x,y,nbins,
image.args = list(col=c(heat.colors(10)[10:1])),
contour.args = list(col="black", lty="solid")){
#---- preceding code snipped ----#
contour.args[[x]] <- contour.args[[y]] <- image.args[[x]] <- image.args[[y]] <- mids
contour.args[[z]] <- image.args[[z]] <- mdata
suppressWarnings(do.call(image, image.args))
#overlay contours
do.call(contour, contour.args)
}
Decomposing this change: instead of ... make a named list of arguments, where the previous hard codes are now defaults. You can then change these items by renaming them in the list or adding to the list. This could be more elegant on the user side, but it gets the job done. Both of the above modifications are untested, but should get you there, and this is all prefaced by my above comment. There may be some other problem that cannot be detected by SO Samaritans because you didn't specify the package or the data.