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

[Jacob Nabe-Nielsen]

Dear Georgi

Thanks a lot for the suggestion. I have now imported rgdal and moved it from Suggests of Imports. However, this did not solve my problem.
I also tried importing 'plot' directly from rgdal, but then I got the error: object ‘plot’ is not exported by 'namespace:rgdal'

Best,
Jacob


> On 14 Apr 2021, at 15.24, Georgi Boshnakov <georgi.boshnakov using manchester.ac.uk> wrote:
> 
>> 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")
> 
> The inclusion of 'library(rgdal)' above suggests that your plot method needs something from 'rgdal'. If that something is a plot method from that package, it may not be visible from your function (due to changes introduced in R-4.0.0, search NEWS for R-4.0.0 'plot'), you would need to import plot methods from rgdal if that is the case (and maybe move rgdal from Suggests to Imports). 
> 
> Georgi Boshnakov
> 
> 
> -----Original Message-----
> From: R-package-devel <r-package-devel-bounces using r-project.org> On Behalf Of Duncan Murdoch
> Sent: 14 April 2021 13:45
> To: Jacob Nabe-Nielsen <jnn using bios.au.dk>; r-package-devel using r-project.org
> Subject: Re: [R-pkg-devel] Problem with S4 method for plotting a raster file
> 
> 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
>> 
>> 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 using landscape, x using type, sep=" - ")
>>             }
>>             # Define colours specific or 'type'
>>             if(missing(col) && x using 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 using crs=="NA") {
>>               crs2 <- sp::CRS(as.character(NA))
>>             } else {
>>               crs2 <- sp::CRS(x using crs)
>>             }
>>             rdata <- raster::raster(x=x using data, xmn=x using ext$xleft, xmx=x using ext$xright,
>>                                     ymn=x using ext$ybottom, ymx=x using ext$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 using crs)
>> rdata <- raster::raster(x = x using data, xmn = x using ext$xleft, xmx = 
>> x using ext$xright, ymn = x using ext$ybottom, ymx = x using ext$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
> 
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