How can I overlay two dense scatter plots so that I can see the outlines of each in R or Matlab?

Question

See this example

This was created in matlab by making two scatter plots indepe

Answer 1

Using ggplot2 you can add together two geom_point's and make them transparent using the alpha parameter. ggplot2 als adds up transparency, and I think this is what you want. This should work, although I haven't run this.

dat = data.frame(x = runif(1000), y = runif(1000), cat = rep(c("A","B"), each = 500))
ggplot(aes(x = x, y = y, color = cat), data = dat) + geom_point(alpha = 0.3)

ggplot2 is awesome!

This is an example of calculating and drawing a convex hull:

library(automap)
library(ggplot2)
library(plyr)
loadMeuse()
theme_set(theme_bw())

meuse = as.data.frame(meuse)
chull_per_soil = ddply(meuse, .(soil), 
           function(sub) sub[chull(sub$x, sub$y),c("x","y")])

ggplot(aes(x = x, y = y), data = meuse) +
  geom_point(aes(size = log(zinc), color = ffreq)) +
  geom_polygon(aes(color = soil), data = chull_per_soil, fill = NA) +
  coord_equal()

which leads to the following illustration: