CODEWITHSUNDEEP
rgraphicsggplot2
Tal Galili
Tal Galili

Reputation: 25306

Plotting a "sequence logo" using ggplot2?

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

Upvotes: 40

Views: 10235

Answers (6)

Omar Wagih
Omar Wagih

Reputation: 8732

ggseqlogo should be what you're looking for. I hope this can relieve some of the frustrations I’m sure many of you have when it comes to plotting sequence logos in R

Upvotes: 14

Omar Wagih
Omar Wagih

Reputation: 8732

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

Upvotes: 4

Ben
Ben

Reputation: 42283

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")

enter image description here

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

Upvotes: 3

Curt F.
Curt F.

Reputation: 4824

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

Upvotes: 12

Zhilong Jia
Zhilong Jia

Reputation: 2359

Here is an alternative option. motiflogo is a new representation of motif (sequence) logo implemented by ggplot2. Two aspects could be considered.

  1. As a canonical motif logo representation
  2. As a SNP-specific motif logo representation

a canonical motif logo representation a SNP-specific motif logo representation

Upvotes: 3

Jeremy Leipzig
Jeremy Leipzig

Reputation: 1944

I have implemented an alternative designed by Charles Berry, which addresses some of the weaknesses of seqLogos discussed ad nauseam in the comment section below. It uses ggplot2:

library("devtools")
install_github("leipzig/berrylogo")
library("berrylogo")
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')))
p<-berrylogo(freqs,gc_content=.41)
print(p)

enter image description here

Upvotes: 10

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