R/dataframe.R

In BradyAJohnston/plasmapR: Create Plasmid Maps in R

.feature_list_to_df <- function(x) {
  # dat <- data.frame(
  #   index = numeric(),
  #   name = character(),
  #   type = character(),
  #   start = numeric(),
  #   end = numeric(),
  #   direction = numeric()
  # )

  feats <- lapply(seq(length(x)), \(i) {
    feat <- x[[i]]

    data.frame(
      index = i,
      name = feat$name,
      type = feat$type,
      start = feat$start_end[1],
      end = feat$start_end[2],
      direction = as.numeric(feat$direction)
    )
  })

  dat <- do.call(rbind, feats)
  # }

  # turn certain features in to numeric columns
  dat$start <- as.numeric(dat$start)
  dat$end <- as.numeric(dat$end)
  dat$direction <- as.numeric(dat$direction)


# only return features where a start was successfully parsed
  # dat[!is.na(dat$start), ]
  dat
}

#' Extract Features of a Plasmid as a DataFrame
#'
#' @param x A list of class 'plasmid' from `read_gb()`
#' @param row.names Ignored.
#' @param optional Ignored.
#' @param ... Ignored.
#'
#' @return a DataFrame
#' @rdname as.data.frame.plasmid
#' @export
as.data.frame.plasmid <- function(x, row.names, optional, ...) {
  .feature_list_to_df(x$features)
}