You can control graph elements with code as you output things from R, but sometimes it is easier to do it manually. Inkscape, an Open Source alternative to Adobe Illustrator, might be what you are looking for.
Filled contour plots are useful for looking at density across two dimensions and are often used to visualize geographic data. It's straightforward to make them in R — once you get your data in the right format, that is.
Color can drastically change how a chart reads and what you see in your data, so don't leave it up to chance with defaults.