Plotting metadata from GenomicRanges object
You can access the data.frame just using $. All of them can be accessed using values() . Something like this:
library(GenomicRanges)
gr = GRanges(seqnames=1,IRanges(start=1:10,width=1))
values(gr) = data.frame(eigen=rnorm(10),ratio=runif(10))

plot(start(gr),gr$eigen)

or
plot(start(gr),values(gr)$eigen)