R/synteny_to_link.R

In thackl/gggenomes: A Grammar of Graphics for Comparative Genomics

#' Helper to extract seqlengths from DECIPHER::FindSyntney Object
#' @keywords internal
#' @param synteny_obj A object produced by DECIPHER::FindSynteny
#' @noRd
get_seqlen <- function(synteny_obj) {
  seqlengths <- c()
  for (i in 1:ncol(synteny_obj)) {
    seqlengths <- c(seqlengths, unlist(.data$synteny[i, i]))
  }
  seqlength_df <- data.frame(
    length = seqlengths,
    fasta_name = names(seqlengths)
  ) %>%
    tibble::remove_rownames()
  seqlength_df
}

#' Format synteny-class into wide tibble This is for use with gggenomes
#' @importFrom methods is
#' @details This function takes a object of class synteny and converts it into a data.frame containing all synteny pairs
#' @param synteny_obj A object produced by DECIPHER::FindSynteny
#' @noRd

synteny_to_link <- function(synteny_obj) {
  if (!is(synteny_obj, "Synteny")) {
    stop("synetny_obj is not of class Synteny")
  }
  seqlengths <- get_seqlen(synteny_obj)
  out_df <- tibble()
  for (iter in c(1:(ncol(synteny_obj) - 1))) {
    tmp_df <- synteny_obj[iter + 1, iter][[1]] %>%
      as.data.frame() %>%
      dplyr::mutate(
        strand = case_when(
          strand == 0 ~ "+",
          TRUE ~ "-"
        ),
        seq_id = (seqlengths[iter, ]$fasta_name %>% stringr::str_extract("[^ ]+")),
        start = .data$start1,
        end = .data$end1,
        length = seqlengths[iter, ]$length,
        seq_id2 = (seqlengths[iter + 1, ]$fasta_name %>% stringr::str_extract("[^ ]+")),
        start2 = .data$start2,
        end2 = .data$end2,
        length2 = seqlengths[iter + 1, ]$length
      ) %>%
      dplyr::select(.data$seq_id, .data$start, .data$end, .data$length, .data$strand, .data$seq_id2, .data$start2, .data$end2, .data$length2)
    out_df <- bind_rows(out_df, tmp_df)
  }
  out_df
}