How can I plot with 2 different y-axes?

Question

I would like superimpose two scatter plots in R so that each set of points has its own (different) y-axis (i.e., in positions 2 and 4 on the figure) but the points appear su

Answer 1

If you can give up the scales/axis labels, you can rescale the data to (0, 1) interval. This works for example for different 'wiggle' trakcs on chromosomes, when you're generally interested in local correlations between the tracks and they have different scales (coverage in thousands, Fst 0-1).

# rescale numeric vector into (0, 1) interval
# clip everything outside the range 
rescale <- function(vec, lims=range(vec), clip=c(0, 1)) {
  # find the coeficients of transforming linear equation
  # that maps the lims range to (0, 1)
  slope <- (1 - 0) / (lims[2] - lims[1])
  intercept <- - slope * lims[1]

  xformed <- slope * vec + intercept

  # do the clipping
  xformed[xformed < 0] <- clip[1]
  xformed[xformed > 1] <- clip[2]

  xformed
}

Then, having a data frame with chrom, position, coverage and fst columns, you can do something like:

ggplot(d, aes(position)) + 
  geom_line(aes(y = rescale(fst))) + 
  geom_line(aes(y = rescale(coverage))) +
  facet_wrap(~chrom)

The advantage of this is that you're not limited to two trakcs.