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.

enter image description here

Personally, I think this is an abomination of a plot, and hope there isn't a way in ggplot2 to do it! — hadley
it would seem that it would be pretty easy to generate a less ugly plot that represented the same information by simply stacking bar plots. You might have to work a little harder to get the annotation on the x axis right. — Ben Bolker
Tal, could you provide some sample data? You could probably just do this with geom_text() — Brandon Bertelsen
These sequence plots are a very common method to represent sequence motifs in biology. I understand that stacked bars could be reasonable for DNA, which only has a 4 letter alphabet, however, for an amino acid sequence the alphabet has 22 letters. — GWW
I think this is an important, commonly used type of plot in bioinformatics, and so I hope there is a way in ggplot2 to do it! — Curt F.

Curt F. Curt F. · Accepted Answer · 2015-03-16T11:32:04

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:

Not bad, but not quite a sequence logo plot

Plotting a "sequence logo" using ggplot2?

6 Answers