R/layout.R

In gggenomes: A Grammar of Graphics for Comparative Genomics

#' Re-layout a genome layout
#'
#' Re-layout the tracks and update the scales after seqs have been modified
#' @param x layout
#' @param ... additional data
#' @return layout with updated scales
#' @export
layout <- function(x, ...) {
  UseMethod("layout")
}

#' @export
layout.gggenomes <- function(x, ignore_seqs = FALSE, ...) {
  x$data <- layout(x$data, ...)
  x
}

#' @export
layout.gggenomes_layout <- function(
    x, ignore_seqs = FALSE, args_seqs = list(),
    args_feats = list(), args_links = list(), ...) {
  if (!ignore_seqs) {
    x <- set_seqs(x, exec(
      layout_seqs, get_seqs(x), !!!args_seqs,
      !!!x$args_seqs
    ))
  }
  # note: tried this with map, but that somehow messes with !!!
  for (i in seq_along(x$feats)) {
    x$feats[[i]] %<>% exec(layout_feats, ., get_seqs(x), !!!args_feats)
  }
  for (i in seq_along(x$links)) {
    x$links[[i]] <- exec(
      as_links, x$orig_links[[i]], get_seqs(x),
      !!!args_links, !!!x$args_links
    )
  }
  x
}

#' Drop a genome layout
#'
#' @param data layout
#' @param ... additional data
#' @return gggenomes object without layout
#' @export
drop_layout <- function(data, ...) {
  UseMethod("drop_layout")
}