The plot works fine for me with the example data you have given. Maybe it is something in your par settings. Try putting a ylim in your plot the same as you have done for the xlim: y1<-min(original.estimate) y2<-max(original.estimate) plot(lfdr.true, original.estimate, pch=19, col = "dark red",xlim = c(x1,x2),ylim=c(y1,y2))