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

No direct way to do so in ggplot2, as far as I'm concerned.

However, check out RWebLogo. It's an R wrapper I have written for the WebLogo python library. You can download it from CRAN and it's hosted on github

Simple example:

# Load package
library('RWebLogo')

# Sample alignment
aln <- c('CCAACCCAA', 'CCAACCCTA', 'AAAGCCTGA', 'TGAACCGGA')
# Plot logo to file
weblogo(seqs=aln, file.out='logo.pdf')

# Plot logo to R graphics device (uses generated jpeg logo and raster package)
weblogo(seqs=aln, plot=TRUE, open=FALSE, format='jpeg', resolution=600)

For more options see ?weblogo or ?plotlogo