Acronym as Sequence Logo

ccbr_seqlogo.png

gattaca_seqlogo.png

mafdash_seqlogo.png

make_custom_seqlogo.R

rm(list=ls())

library(ggseqlogo)
set.seed(1234)

myletters <- "CCBR"
# myletters <- "NCBR"

letter_vec <- unlist(strsplit(toupper(myletters),""))
allletters <- unique(c("A","T","G","C",letter_vec))
custom_mat <- matrix(0,nrow=length(allletters), ncol=length(letter_vec))
rownames(custom_mat) <- allletters

big_size=1
for (pos_idx in 1:ncol(custom_mat)) {
  # pos_idx=1
  big_row=which(rownames(custom_mat) %in% letter_vec[pos_idx])
  little_rows=which(rownames(custom_mat) %in% setdiff(c("A","T","G","C"), letter_vec[pos_idx]))
  custom_mat[big_row,pos_idx] <- big_size
  
  little_min_size=big_size*0.05
  little_max_size=big_size*0.3
  custom_mat[little_rows,pos_idx] <- -runif(length(little_rows), little_min_size, little_max_size)
  
}


# Generate sequence logo
ggseqlogo(custom_mat, method='custom', namespace=allletters) +
  ylab("")+theme(axis.text.x = element_blank(),
                 axis.text.y = element_blank(),
                 axis.ticks = element_blank())