[R-pkg-devel] Problem with S4 method for plotting a raster file

Hi Duncan

Thanks a lot for the help. This works, but unfortunately it does not 
result in a landscape which is cropped to the extent of the bathymetry 
raster file... it would be nice to be able to do that as well (as you 
can if you use the 'raster' and 'sp' packages).

Best wishes,
Jacob

On 14 Apr 2021, at 14.44, Duncan Murdoch <murdoch.duncan at gmail.com 
<mailto:murdoch.duncan at gmail.com>> wrote:

On 14/04/2021 5:41 a.m., Jacob Nabe-Nielsen wrote:

Dear all,
I have just discovered an error in a package that I have already 
uploaded to
CRAN, and cannot figure out how to fix it. All help will be greatly 
appreciated.
The package is called DEPONS2R, and is available from:
https://cran.r-project.org/web/packages/DEPONS2R/index.html 
<https://cran.r-project.org/web/packages/DEPONS2R/index.html>
The problem is related to one of the included examples, where I plot 
the coastline
on top of a raster file. In the example, where the plotting is 
embedded in
an S4 method called plot.DeponsRaster, the coastline does not show. 
But if
I run the functions that the method is composed of, everything works 
fine (see
below). So I am wondering if the graphics devise is not passed on 
correctly
within the package, or what actually happens.
The example that does not run correctly is available from 
?plot.DeponsRaster:
library(DEPONS2R)
data("bathymetry")
plot(bathymetry)
data("coastline")
library(rgdal)
# Change projection of coastline to match that of bathymetry data
coastline2 <- spTransform(coastline, crs(bathymetry))
plot(coastline2, add=TRUE, col="lightyellow2")
Here the coastline is not plotted. The method is defined as:
setMethod("plot", signature("DeponsRaster", "ANY"),
??????????function(x, y, maxpixels=500000, col, alpha=NULL, colNA=NA, 
add=FALSE,
???????????????????ext=NULL, useRaster=TRUE, interpolate=FALSE, 
addfun=NULL,
???????????????????nc, nr, maxnl=16, main, npretty=0, axes=TRUE,
???????????????????legend=TRUE, trackToPlot=1, ...) ?{
????????????oldpar <- graphics::par(no.readonly = TRUE)
????????????on.exit(graphics::par(oldpar))
????????????if (missing(main)) {
??????????????main <- paste(x at landscape, x at type, sep=" - ")
????????????}
????????????# Define colours specific or 'type'
????????????if(missing(col) && x at type=="bathymetry") {
??????????????tmp.col <- grDevices::rainbow(1000)[501:800]
??????????????col <- c(tmp.col[1:100], rep(tmp.col[101:250], each=5))
????????????}
????????????# Use {raster}-package for plotting
????????????if(x at crs=="NA") {
??????????????crs2 <- sp::CRS(as.character(NA))
????????????} else {
??????????????crs2 <- sp::CRS(x at crs)
????????????}
????????????rdata <- raster::raster(x=x at data, xmn=x at ext$xleft, 
xmx=x at ext$xright,
????????????????????????????????????ymn=x at ext$ybottom, ymx=x at ext$ytop,
????????????????????????????????????crs=crs2)
????????????raster::plot(rdata, col=col, main=main,
?????????????????????????alpha=alpha, add=add, ext=ext, axes=axes, 
legend=legend)
??????????}
)
But when I use the functions that are at the core of this method it is
not a problem adding the coastline correctly:
x <- bathymetry
crs2 <- raster::crs(x at crs)
rdata <- raster::raster(x = x at data, xmn = x at ext$xleft,
xmx = x at ext$xright, ymn = x at ext$ybottom, ymx = x at ext$ytop,
crs = crs2)
raster::plot(rdata)
plot(coastline2, add=TRUE, col="lightyellow2")
If would be fantastic if someone can figure out how I should modify 
the method
to plot the coastline correctly on top of the map.

I'm not sure exactly what is going wrong, but if you plot the 
coastline first and the bathymetry second, things do show up. ?Maybe 
that's enough of a hint for you:

library(DEPONS2R)
data("coastline")
library(rgdal)
coastline2 <- spTransform(coastline, crs(bathymetry))
plot(coastline2, col="lightyellow2")

data("bathymetry")
plot(bathymetry, add=TRUE)

This puts the legend on top of the plotted coastline data, so my guess 
is that the limits of the bathymetry plot aren't being made available 
to the coastline plot when you do things in the original order.

Duncan Murdoch