Color code points based on percentile in ggplot

Question

I have some very large files that contain a genomic position (position) and a corresponding population genetic statistic (value). I have successfully plotted these values and wo

Answer 1

This is how I would approach it - basically creating a factor defining which group each observation is in, then mapping colour to that factor.

First, some data to work with!

dat <- data.frame(key = c("a1-a3", "a1-a2"), position = 1:100, value = rlnorm(200, 0, 1))
#Get quantiles
quants <- quantile(dat$value, c(0.95, 0.99))

There are plenty of ways of getting a factor to determine which group each observation falls into, here is one:

dat$quant  <- with(dat, factor(ifelse(value < quants[1], 0, 
                                  ifelse(value < quants[2], 1, 2))))

So quant now indicates whether an observation is in the 95-99 or 99+ group. The colour of the points in a plot can then easily be mapped to quant.

ggplot(dat, aes(position, value)) + geom_point(aes(colour = quant)) + facet_wrap(~key) +
  scale_colour_manual(values = c("black", "blue", "red"), 
                      labels = c("0-95", "95-99", "99-100")) + theme_bw()