Thank you Thomas for your response. I got the solution I was looking for from Martin Morgan: ********** Lauri -- I flattened your z and added 'Sib' and 'Location' > snps <- data.frame(Sib=rep(seq(1, ncol(z)), each=nrow(z)), + gtype=as.vector(z), + Location=snploc$location) I then created a vector of colours, using that to colour each point in a dot plot: > colours <- c("blue", "red", "black") > library(lattice) > dotplot(Sib~Location, snps, col=colours[snps$gtype]) (adding pch="|", cex=2 makes a plot similar to yours, with vertical bars at each SNP, other point types provide different effects). Martin ********** Best regards, Lauri FRCBS