r - 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 wondering if there could be a ggplot2 version of it.

Thanks.

Answer 1

I'm submitting a ggplot2 attempt that is somewhat similar to the Leipzig/Berry solution above. This format is a little bit closer to the standard logogram.

But my solution, and I think any ggplot2 solution, still falls short because ggplot2 does not offer control over the aspect ratio of plotting symbols. This is the core capability that (I think) is required for generating sequence logos and that is missing from ggplot2.

Also note: I used the data from Jeremy Leipzig's answer, but I did not do any corrections for small sample sizes or for %GC values different than 50%.

require(ggplot2)
require(reshape2)

 freqs<-matrix(data=c(0.25,0.65,0.87,0.92,0.16,0.16,0.04,0.98,0.98,1.00,0.02,0.10,0.10,0.80,0.98,0.91,0.07,0.07,0.11,0.05,0.04,0.00,0.26,0.17,0.00,0.01,0.00,0.00,0.29,0.17,0.01,0.03,0.00,0.00,0.32,0.32,0.53,0.26,0.07,0.02,0.53,0.18,0.96,0.01,0.00,0.00,0.65,0.01,0.89,0.17,0.01,0.09,0.59,0.12,0.11,0.04,0.02,0.06,0.05,0.49,0.00,0.00,0.02,0.00,0.04,0.72,0.00,0.00,0.01,0.00,0.02,0.49),byrow=TRUE,nrow=4,dimnames=list(c('A','C','G','T')))

freqdf <- as.data.frame(t(freqs))

freqdf$pos = as.numeric(as.character(rownames(freqdf)))

freqdf$height <- apply(freqdf[,c('A', 'C','G','T')], MARGIN=1,
                       FUN=function(x){2-sum(log(x^x,base=2))})

logodf <- data.frame(A=freqdf$A*freqdf$height, C=freqdf$C*freqdf$height,
                     G=freqdf$G*freqdf$height, T=freqdf$T*freqdf$height, 
                     pos=freqdf$pos)

lmf <- melt(logodf, id.var='pos')

quartz(height=3, width=8)

ggplot(data=lmf, aes(x=as.numeric(as.character(pos)), y=value))  +
    geom_bar(aes(fill=variable,order=value), position='stack', 
        stat='identity', alpha=0.5) +
    geom_text(aes(label=variable, size=value, order=value, vjust=value),
        position='stack') +
    theme_bw()

quartz.save('StackOverflow_5438474.png', type='png')

That produces this graph: