Clip depth contour with spatial polygon

Question

I need to somehow combine my Spatialpolygons with my depth contour, but not sure how do to so. Maybe create a SpatialPolygonsDataframe?

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 (not sure if this is the best way to achieve what I want)
    extent(raster_bath) <- extent(subarea0)#Transform the extend of my raster to the extend of my SpatialPolygons
v <- extract(raster_bath, subarea0)#Extract data from my Raster Layer for the locations of my SpatialPolygons

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

EDITS

I apologize in advance, looks like I've been having a hard time to explain clearly what I was hoping to get. I don't want to summarize my depth info for each of my polygon but rather provide a detailed bathymetry within my area of interest. I am definitely not sure if what I did up to now is the way to go, but ultimately what I would like to achieve is to end-up with a plot of my polygon with my depth information. Something like this (thanks to Simbamangu), but without the depth info outside of my polygon. Basically, I just want the bathymetry info comprise in my overall area at the finest scale possible. Should I first transform my SpatialPolygons into one and then into some grid format to then be able to clip with my raster layer?

Thank you!

Answer 1

Slightly different approach to first question ... you'll need to create SpatialLines (or a SpatialLinesDataFrame) and work with that.

library(maptools) # Contour tools
library(marelac) # bathymetry data
library(raster) # only used for displaying Bathymetry here
library(rgeos) # for intersections

cont <- contourLines(Bathymetry$x, Bathymetry$y, Bathymetry$z) # generate contours
c.lines <- ContourLines2SLDF(cont) # create SpatialLines DF

#Have a look:
b.rast <- raster(Bathymetry) 
plot(b.rast) # plot world bathymetry
lines(c.lines) # our SpatialLines overlap and look OK

# Clip to your boundary
subarea0 <- readShapePoly("subarea0.shp") 
subarea0.lines <- gIntersection(c.lines, subarea0) # clip the contours to subarea0
plot(subarea0)
plot(subarea0.lines)

Answer 2

v is a list. There is one list element for each polygon. Each list element can have many values (one for each raster cell that it covers). Therefore, you cannot simply combine the data to the SpatialPolygons (and you are not saying why you want to do that anyway). To get a single value for each polygon, you can use extract with a function (mean would be the natural choice)

vv <- extract(raster_bath, subarea0, fun=mean)

or use lapply with v, something like this:

vvv <- lapply(v, mean, na.rm=TRUE) 

turn that into a data.frame and use function SpatialPolygonsDataFrame to create that type of object.