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rcharacterfrequency-distribution

Count letter frequencies in descending order

I have a data looks like this 

df<-structure(list(col = structure(c(9L, 2L, 13L, 11L, 5L, 7L, 10L, 
6L, 8L, 3L, 12L, 4L, 1L), .Label = c("HHRGGVCTS", "MGSSN", "MVKTTYYDVG", 
"RRHYNGAYDD", "RTSTN", "S", "SNCWC", "sp|P31689|DNJA1_HUMAN DnaJ homolog GN=DNAJA1 PE=1 SV=2  ", 
"sp|Q9H9K5|MER34_HUMAN Endogenous PE=1 SV=1", "THYDT", "TVHAV", 
"VCMCVVDDNR", "YATTA"), class = "factor")), class = "data.frame", row.names = c(NA, 
-13L))

I am trying to count letter frequencies. There are 20 possible letters which I want to count in each row.

For example,

  1. the first row: row starts with sp| so character frequencies are not calculated and result is the original string
  2. the second row: doesn't start with sp| so it will show character frequencies
MGSSN  2,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0

which means, there are 2 S, 1, M, 1, G, 1, N and the other letters are empty .

The character frequencies are ordered in descending order.

The final output would look like the following 

output<-structure(list(col = structure(c(9L, 2L, 13L, 11L, 5L, 7L, 10L, 
6L, 8L, 3L, 12L, 4L, 1L), .Label = c("HHRGGVCTS", "MGSSN", "MVKTTYYDVG", 
"RRHYNGAYDD", "RTSTN", "S", "SNCWC", "sp|P31689|DNJA1_HUMAN DnaJ homolog GN=DNAJA1 PE=1 SV=2  ", 
"sp|Q9H9K5|MER34_HUMAN Endogenous PE=1 SV=1", "THYDT", "TVHAV", 
"VCMCVVDDNR", "YATTA"), class = "factor"), Col2 = structure(c(8L, 
2L, 3L, 2L, 2L, 2L, 2L, 1L, 7L, 5L, 6L, 5L, 4L), .Label = c("1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 
"2,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", "2,2,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0", 
"2,2,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0", "2,2,2,1,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0", 
"3,2,2,1,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0", "sp|P31689|DNJA1_HUMAN DnaJ homolog GN=DNAJA1 PE=1 SV=2  ", 
"sp|Q9H9K5|MER34_HUMAN Endogenous PE=1 SV=1"), class = "factor")), class = "data.frame", row.names = c(NA, 
-13L))
Solution

  • We can use str_count

    library(stringr)
i1 <- !grepl("^sp", df$col)
df$col2[i1] <- sapply(as.character(df$col[i1]), function(x)
     paste(sort(str_count(x, LETTERS), decreasing = TRUE), collapse=", "))
df$col2[!i1] <- df$col[!i1]

    Or instead of keeping as a string, it can be a list column as well

    library(tidyverse)
df %>%
    mutate(col = as.character(col),
            col2 = map(col, ~ if(str_detect(.x, "^sp")) .x 
               else str_count(.x, LETTERS) %>% 
             sort(decreasing = TRUE)))