berrylogo: a better sequence logo
A berrylogo is a sequence logo alternative developed by Charles C. Berry for "Selection of Target Sites for Mobile DNA Integration in the Human Genome" [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1664696/)
Instead of “information content”, the y-axis is the log relative frequency with respect to the background frequency, generated here from the gc_content parameter.
# Install latest commit from Github: 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)