R/create_table_mutation.R

In maous1/Pandem2simulator: Data simulator for Pandem2

#' create_table_mutation
#'
#' @param nextclade_data
#'
#' @return
#' @export create_table_mutation
#'
#' @examples
create_table_mutation <- function(nextclade_data) {
  alldata <- data.frame()
  for (i in 1:dim(nextclade_data)[1]) {
    current <- nextclade_data[i, ]

    frame <- data.frame(substitutions = unlist(strsplit(current$substitutions, split = ","))) %>%
      mutate(place = gsub("[^0-9]", "", substitutions)) %>%
      mutate(nucleotide = gsub("[0-9]", "", substitutions))  %>%
      filter(between(x = as.numeric(place),left = 21563,right = 25384)) %>%
      select(-substitutions) %>%
      pivot_wider(names_from = "place", values_from = "nucleotide")

    current <- tibble::data_frame(current, frame) %>% select(-substitutions)
    alldata <- union_all(alldata, current)
  }

  alldata_deletion <- data.frame()
  for (i in 1:dim(nextclade_data)[1]) {
    current <- alldata[i, ]
    frame_deletion <- data.frame(deletions = unlist(strsplit(current$deletions, ","))) %>%
      group_by(deletions) %>%
      mutate(start = as.numeric(unlist(strsplit(deletions, "-"))[1])) %>%
      mutate(end = as.numeric(unlist(strsplit(deletions, "-"))[2])) %>%
      mutate(end = ifelse(is.na(end), start, end))


    frame_missing <- data.frame(missing = unlist(strsplit(current$missing, ","))) %>%
      group_by(missing) %>%
      mutate(start = as.numeric(unlist(strsplit(missing, "-"))[1])) %>%
      mutate(end = as.numeric(unlist(strsplit(missing, "-"))[2])) %>%
      mutate(end = ifelse(is.na(end), start, end))

    if (nrow(frame_deletion) != 0) {
      vecteur_deletion <- c()
      for (k in 1:length(frame_deletion$end)) {
        vecteur_deletion <- c(vecteur_deletion, frame_deletion$start[k]:frame_deletion$end[k])
      }
      common <- intersect(names(current), as.character(vecteur_deletion))
      current[common] <- "deletion"
    }
    if (nrow(frame_missing) != 0) {
      vecteur_missing <- c()
      for (k in 1:length(frame_missing$end)) {
        vecteur_missing <- c(vecteur_missing, frame_missing$start[k]:frame_missing$end[k])
      }
      common <- intersect(names(current), as.character(vecteur_missing))
      current[common] <- "missing"
    }
    alldata_deletion <- union_all(alldata_deletion, current)
  }

  alldata_deletion <- alldata_deletion %>%
    filter(!is.na(time)) %>%
    mutate_all(~ replace(., is.na(.), "wild type")) %>%
    select(-c(missing, deletions, insertions))

  return(alldata_deletion)
}