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 independently, creating images of each, then using the imagesc to draw them into the same figure and then finally setting the alpha of the top image to 0.5.

I would like to do this in R or matlab without using images, since creating an image does not preserve the axis scale information, nor can I overlay a grid (e.g. using 'grid on' in matlab). Ideally I wold like to do this properly in matlab, but would also be happy with a solution in R. It seems like it should be possible but I can't for the life of me figure it out.

So generally, I would like to be able to set the alpha of an entire plotted object (i.e. of a matlab plot handle in matlab parlance...)

Thanks,

Ben.

EDIT: The data in the above example is actually 2D. The plotted points are from a computer simulation. Each point represents 'amplitude' (y-axis) (an emergent property specific to the simulation I'm running), plotted against 'performance' (x-axis).

EDIT 2: There are 1796400 points in each data set.

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: