I agree with you. I think it's better to use transparency to show density-- here's an example from ggplot2: http://had.co.nz/ggplot2/graphics/25464f1f2c009d435b

I agree with you. I think it's better to use transparency to show density-- here's an example from ggplot2: http://had.co.nz/ggplot2/graphics/25464f1f2c009d435b862debcad8db51.png http://had.co.nz/ggplot2/graphics/25464f1f2c009d435b862debca... and the page in general at http://had.co.nz/ggplot2/geom_point.html http://had.co.nz/ggplot2/geom_point.html And if you do this overplotting with partly transparent data points, you can even continue using scatterplots (which have several benefits over binned color density plots, such as showing the actual data, rather than summaries).