How to rasterize SpatialPolygons in R?

Question

I'm trying to extract the bathymetry values of my area of interest from a world bathymetry raster layer using the 'rasterize' function in the {sp} package.

*Edits: I found the 'extract' function which seems to be more what I'm looking for.

This is what I've done so far:

> class(subarea0) #This is my area of interest (Eastern Canadian Arctic Sea)
[1] "SpatialPolygons"
attr(,"package")
[1] "sp"

> extent(subarea0)
class       : Extent 
xmin        : -82.21997 
xmax        : -57.21667 
ymin        : 60.2 
ymax        : 78.16666

library(marelac)
data("Bathymetry")#World bathymetric data in library (marelac)
names(Bathymetry);class(Bathymetry);str(Bathymetry)
[1] "x" "y" "z"
[1] "list"
List of 3
 $ x: num [1:359] -180 -179 -178 -177 -176 ...
 $ y: num [1:180] -89.5 -88.5 -87.5 -86.5 -85.5 ...
 $ z: num [1:359, 1:180] 2853 2873 2873 2873 2873 ...

  raster_bath<-raster(Bathymetry)#Transformed into a raster layer
    extent(raster_bath) <- extent(subarea0)#Transform the extend of my raster to the extend of my SpatialPolygons

>ras_sub0<-rasterize(subarea0,raster_bath)#rasterize my SpatialPolygons (*Edits: not the function that I need here, but I am still interested to learn what results mean)
Found 2 region(s) and 10 polygon(s)
> plot(ras_sub0)
> plot(subarea0, add=TRUE)

> ras_sub0
class       : RasterLayer 
dimensions  : 180, 359, 64620  (nrow, ncol, ncell)
resolution  : 0.06964709, 0.0998148  (x, y)
extent      : -82.21997, -57.21667, 60.2, 78.16666  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +ellps=WGS84 
values      : in memory
min value   : 1 
max value   : 2 
layer name  : layer 

I don't understand the result. Why am I getting 2 colors for each of my polygons? What do they mean?

How can I ultimately get bathymetry depth contour? Is this something to do with my resolution or changing the dimensions?

*Edits: ok, I've now done the following:

v <- extract(raster_bath, subarea0)#Extract data from my Raster Layer for the locations of my SpatialPolygons

v is a list and I am not quiet sure how/under what form to rebind this info with my spatial polygon.

Answer 1

Your line ras_sub0<-rasterize(subarea0,raster_bath) is just taking the index number of the polygons and assigning that to the values of the raster.

If you want just the intersection of your polygon and the raster:

subarea0_bathy <- intersect(raster_bath, subarea0)

Update: As @GodinA notes, looks like intersect() sometimes doesn't return a raster that has the complete extent of the polygon! To get around this, you can intersect with a slightly larger raster than your original:

r2 <- raster() # create a generic raster
extent(r2) <- extent(subarea0) + 1 # add 1 degree of extent (0.5 each side)
r3 <- intersect(raster_bath, r2) 

Answer 2

Here is another solution, using a basic subset function in raster.

# create a raster with the dimensions that you are interested in.
r <- raster(extent(subarea0)+1) # +1 to increase the area
res(r) <- 0.1 # you can change the resolution here. 0.1 can be about 10x10 km if you are close to the equator.
crs(r) <- projection(subarea0) # transfer the coordinate system to the raster

# Now you can add data to the cells in your raster to mark the ones that fall within your polygon.
r[subarea0,] <- 1 # this an easy way to subset a raster using a SpatialPolygons object

# check your raster
plot(r)