Question

I have analysed a dataset of GPS points using density.ppp to generate a sort of heatmap of intensity of the points, as shown below:

However, I would like the image to be limited to the borders of the shapefile, similar to below:

The first image is called as

x <- readShapePoly("dk.shp")
xlim<-c(min(912),max(920))
ylim<-c(min(8023),max(8030))
a<-ppp(cases@coords[,1], cases@coords[,2], xlim, ylim, unitname=c("km"))
plot(density.ppp(a, 0.1), col=COLORS)
plot(x, add=T, border="white")

where cases@coords are the GPS coordinates of each point of interest, and x is a shapefile which provides the outline for the geographical unit.

The second image is called using this code:

plot(x, axes=T, col=COLORS, border="White")

Does anyone know how this might be done? Perhaps it’s not possible with plot() and I will need another package.

As an aside, the next step I plan to do will be to overlay this image over a map imported from GoogleEarth. I’m not yet sure how to do that either, but will post the answer if and when I work it out

many thanks

Answer 1

The result of density.ppp has a matrix (v) that contains the information, if the points outside of the polygon of interst are changed to NA before it is plotted then they will not plot. Here is an example of doing this:

library(maptools)
library(sp)
library(spatstat)

xx <- readShapePoly(system.file("shapes/sids.shp", package="maptools")[1],
      IDvar="FIPSNO", proj4string=CRS("+proj=longlat +ellps=clrk66"))

x <- rnorm(25, -80, 2)
y <- rnorm(25, 35, 1 )

tmp <- density( ppp(x,y, xrange=range(x), yrange=range(y)) )
plot(tmp)
plot(xx, add=TRUE)
points(x,y)

tmp2 <- SpatialPoints( expand.grid( tmp$yrow, tmp$xcol )[,2:1],
    proj4string=CRS(proj4string(xx)) )

tmp3 <- over( tmp2, xx )

tmp$v[ is.na( tmp3[[1]] ) ] <- NA

plot(tmp)
plot(xx, add=TRUE)