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

AFAIK, your best option with Matlab is to just make your own plot function. The scatter plot points unfortunately do not yet have a transparency attribute so you cannot affect it. However, if you create, say, most crudely, a bunch of loops which draw many tiny circles, you can then easily give them an alpha value and obtain a transparent set of data points.