library(raster)
r <- raster(nrows=3,ncols=2,xmn=0,xmx=2,ymn=0,ymx=3,vals=1:6)
colors <- c('red','orange','yellow','green','blue','purple')
plot(r,col=colors)

r1 <- crop(r,extent(c(0.5,1.5,0.5,1.5)))
plot(r1,col=colors)

> values(r)
[1] 1 2 3 4 5 6
> values(r1)
[1] 3 4 5 6