R/epivizToGviz.R

In HCBravoLab/epivizGviz: Convert epivizr workspaces to GViz plots, and viceversa

#' Convert an existing Epiviz workspace into a Gviz plot.
#'
#' @param app (EpivizApp) an object of class \code{\link[epivizr]{EpivizApp}}.
#' @param plot_tracks (logical) plot all of the Gviz tracks together.
#'
#' @return A list of GdObjects that represent Gviz tracks, ex: \code{\link[Gviz]{GeneRegionTrack}}, \code{\link[Gviz]{AnnotationTrack}}, \code{\link[Gviz]{DataTrack}}
#'
#' @examples
#' # see package vignette for example usage
#' \dontrun{
#' epivizToGviz(app, plot_tracks=TRUE)
#' }
#'
#' @import Gviz
#' @export
epivizToGviz <- function(app, plot_tracks=TRUE) {

  # check arguments
  if (!is(app, "EpivizApp")) {
    stop("'app' must be an 'EpivizApp' object")
  }

  # callback for location
  if (app$is_server_closed()) {
    stop("The server for 'app' is closed")
  }

  loc <- NULL
  app$get_current_location(function(response) {
    if (response$success) {
      loc <<- response$value
    }})
  chr <- loc$seqName
  start <- loc$start
  end <- loc$end

  # get chart ids and chart objects
  track_list <- list()
  chart_ids <- ls(envir=app$chart_mgr$.chart_list)
  for (id in chart_ids) {
    chart_obj <- app$chart_mgr$.get_chart_object(id)
    type <- chart_obj$.type
    # create gviz objects
    if (type=="epiviz.plugins.charts.GenesTrack") {
      track_list[[length(track_list)+1]] <- convertEpivizGenes(app=app, chart_obj=chart_obj, chr=chr)
    } else if (type=="epiviz.plugins.charts.BlocksTrack") {
      track_list[[length(track_list)+1]] <- convertEpivizBlocks(app=app, chart_obj=chart_obj, chr=chr)
    } else if (type=="epiviz.plugins.charts.LineTrack" || type=="epiviz.plugins.charts.LinePlot") {
      track_list[[length(track_list)+1]] <- convertEpivizLine(app=app, chart_obj=chart_obj, chr=chr)
    } else if (type=="epiviz.plugins.charts.StackedLineTrack" || type=="epiviz.plugins.charts.StackedLinePlot") {
      track_list[[length(track_list)+1]] <- convertEpivizStackedLine(app=app, chart_obj=chart_obj, chr=chr)
    } else if (type=="epiviz.plugins.charts.HeatmapPlot") {
      track_list[[length(track_list)+1]] <- convertEpivizHeatmap(app=app, chart_obj=chart_obj, chr=chr)
    } else if (type=="epiviz.plugins.charts.ScatterPlot") {
      track_list[[length(track_list)+1]] <- convertEpivizScatter(app=app, chart_obj=chart_obj, chr=chr)
    }
  }
  track_list <- unique(unlist(track_list))

  # adjust plot sizes
  size <- list()
  for (track in track_list) {
    if (class(track)=="IdeogramTrack") {
      size[[length(size)+1]] <- 1
    } else if (class(track)=="GenomeAxisTrack") {
      size[[length(size)+1]] <- 2
    } else if (class(track)=="GeneRegionTrack") {
      size[[length(size)+1]] <- 1
    } else if (class(track)=="AnnotationTrack") {
      size[[length(size)+1]] <- 2
    } else if (class(track)=="DataTrack") {
      size[[length(size)+1]] <- 6
    }
  }

  # plot list of converted tracks
  if (plot_tracks==TRUE) {
  plotTracks(track_list, from=start, to=end, sizes=size)
  }

  return(track_list)
}