gistfile1.r

> p <- ggplot(data=masterdata8, aes(certainty, nanoseconds, colour="red")) + 
> geom_point() + 
> geom_point(data=masterdata4, colour="blue") + 
> geom_point(data=masterdata1, colour="green")



> head(masterdata8)
  certainty             benchmark iterations nanoseconds
1        10 BenchmarkSafePrimes-8         10 13465462805
2        11 BenchmarkSafePrimes-8         10 14741964114
3        12 BenchmarkSafePrimes-8         10 16018608344
4        13 BenchmarkSafePrimes-8          5 14646835899
5        14 BenchmarkSafePrimes-8          5 15734636602
6        15 BenchmarkSafePrimes-8          5 16736838514

You could also try this:

masterdata <- rbind(masterdata1, masterdata4, masterdata8)
p <- ggplot(data=masterdata, aes(certainty, nanoseconds, color=benchmark)) +
       geom_point() +
       scale_colour_manual(values = c('red', 'blue', 'green'), breaks=...)