I believe @ technocrat was suggesting doing all the plotting in ggplot2 rather than in base graphics.
I think you are correct that the data should not be separated but I am not familiar with the type of analysis you are doing. Unless there is a huge amound of code, it might be better to post sone sample raw data and your code for readers to get a feel for what you are doing overall. BTW, you did do the initial analysis in R?