R/SequenceDataSet-viz.R

In RNAmodR: Detection of post-transcriptional modifications in high throughput sequencing data

#' @include RNAmodR.R
#' @include SequenceDataSet-class.R
NULL

#' @rdname plotData
#' @export
setMethod(
  f = "getDataTrack",
  signature = signature(x = "SequenceDataSet"),
  definition = function(x, name = name, ...) {
    sdts <- lapply(x,
                   function(z){
                     getDataTrack(z, name = name, ...)
                   })
    sdts <- unname(sdts)
    do.call(c,sdts)
  }
)


#' @rdname plotData
#' @export
setMethod(
  f = "plotDataByCoord",
  signature = signature(x = "SequenceDataSet", coord = "GRanges"),
  definition = function(x, coord, type = NA, window.size = 15L, ...) {
    # input check
    coord <- .norm_coord_for_visualization(ranges(x), coord)
    from_to <- .get_viz_from_to_coord(ranges(x), coord, window.size)
    plotData(x, name = coord$Parent, from = from_to$from,
                  to = from_to$to, type = type, ...)
  }
)

#' @rdname plotData
#' @importFrom Gviz plotTracks
#' @export
setMethod(
  f = "plotData",
  signature = signature(x = "SequenceDataSet"),
  definition = function(x, name, from, to, perTranscript = FALSE, 
                        showSequence = TRUE, showAnnotation = FALSE, ...) {
    # get plotting arguments
    args <- .norm_viz_args_SequenceData(list(...), x)
    chromosome <- .norm_viz_chromosome(ranges(x), name)
    from_to <- .get_viz_from_to(ranges(x), name, from, to)
    showSequence <- .norm_show_argument(showSequence, TRUE)
    showAnnotation <- .norm_show_argument(showAnnotation, FALSE)
    # get tracks
    atm <- NULL
    st <- NULL
    if(showAnnotation){
      atm <- .get_viz_annotation_track(x, args)
    }
    if(showSequence){
      st <- .get_viz_sequence_track(sequences(x)[name], ranges(x)[name],
                                    chromosome, args)
    }
    dts <- getDataTrack(x, name = name, ...)
    tracks <- c(dts,list(st,atm))
    # plot tracks
    tracks <- tracks[!vapply(tracks, is.null, logical(1))]
    do.call(Gviz::plotTracks,
            c(list(tracks, from = from_to$from, to = from_to$to,
                   chromosome = chromosome),
              args[["plot.pars"]]))
  }
)