R/augment_barracoda_data.R

In leonjessen/Barracoda2viz:

augment_barracoda_data = function(x){

  # Get original peptides for each sample
  originals = x %>% get_original_peptide

  # Split the data into mutation data and original data
  mut_dat = x %>% filter(pep.number %>% str_detect("original") %>% `!`)
  org_dat = x %>% filter(pep.number %>% str_detect("original"))

  # Create augmented mutation data
  mut_dat_aug = mut_dat %>% get_mut_pos %>% get_mut_res %>% mutate(pep_type = 'mutant')

  # Get unique samples
  samples = originals %>% pull(sample)

  # Create augmented original data
  org_dat_aug = tibble()
  for( id in samples ){
    org = originals %>% filter(sample==id) %>% pull(original)
    for( i in 1:nchar(org) ){
      res = org %>% str_sub(start = i, end = i)
      tmp = org_dat %>% filter(sample == id) %>%
        mutate(mut_pos = i,
               mut_res_three = res %>% residue_name(to = 'three'),
               mut_res_one = res,
               pep_type = 'original')
      org_dat_aug = org_dat_aug %>% bind_rows(tmp)
    }
  }

  # Merge augmented mutation data with augmented original data
  d_clean_aug = mut_dat_aug %>% bind_rows(org_dat_aug) %>%
    arrange(sample,mut_res_three,mut_pos)

  # Done, return!
  return(d_clean_aug)
}