I was able to produce a 12 by 10 panel graph using the lattice
package. Hopefully it can get you headed in the right direction.
> roots <-read.table("COBS Roots 2008-2013noCNfake08.txt", header = TRUE)
> roots$EU <- with(roots, factor(plot):factor(depth))
> library(lattice)
> xyplot(mass ~ year | EU, data = roots, layout = c(12,10))