Plotting a “sequence logo” using ggplot2?

Question

Is it (reasonably) possible to plot a sequence logo plot using ggplot2?

There is a package to do it which is based on \"grid\" called \"seqLogo\", but I was wonderin

Answer 1

There is now a gglogo package (also on CRAN, yet another amazing ggplot2 extension by Heike Hofmann).

This package that produces plots like these:

library(ggplot2)
library(gglogo)
ggplot(data = ggfortify(sequences, "peptide")) +      
  geom_logo(aes(x=position, y=bits, group=element, 
     label=element, fill=interaction(Polarity, Water)),
     alpha = 0.6)  +
  scale_fill_brewer(palette="Paired") +
  theme(legend.position = "bottom")

The example is from https://github.com/heike/gglogo/blob/master/visual_test/logos.R and there's a manuscript on the package here: https://github.com/heike/logopaper/blob/master/logos.Rmd