IanCal's comment about setting the alpha is a good one. Another easy option is to make a heatmap of 2D bin counts. Since you're using R already, you can use ggp

IanCal's comment about setting the alpha is a good one. Another easy option is to make a heatmap of 2D bin counts. Since you're using R already, you can use ggplot for this: http://docs.ggplot2.org/current/geom_bin2d.html http://docs.ggplot2.org/current/geom_bin2d.html