The familiar but underused layout is a good way to look at patterns over time. This tutorial gives you an easy way to make them and guides you through the code so you can adapt it to your needs.
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.