How to produce a meaningful draftsman/correlation plot for discrete values

One of my favorite tools for exploratory analysis is pairs(), however in the case of a limited number of discrete values, it falls flat as the dots all align perfectly. Consider the following:

y <- t(rmultinom(n=1000,size=4,prob=rep(.25,4)))
pairs(y)

It doesn't really give a good sense of correlation. Is there an alternative plot style that would?

Solution

If you change y to a data.frame you can add some 'jitter' and with the col option you can set the transparency level (the 4th number in rgb):

y <- data.frame(y)
pairs(sapply(y,jitter), col = rgb(0,0,0,.2))

enter image description here

Or you could use ggplot2's plotmatrix:

library(ggplot2)
plotmatrix(y) + geom_jitter(alpha = .2)

enter image description here

Edit: Since plotmatrix in ggplot2 is deprecated use ggpairs (GGally package mentioned in @hadley's comment above)

library(GGally)
ggpairs(y, lower = list(params = c(alpha = .2, position = "jitter")))

enter image description here