load a splice junction track from a data.frame

load splice junctions held in R. The table is written as the six-column bed igv.js draws junctions from, and served from the same directory as the other local-data tracks.

Coordinates are taken as bed coordinates and written out unchanged, as the other *FromLocalData loaders take theirs. STAR reports the first and last intron base of a junction 1-based in SJ.out.tab, so a table read straight from that file needs its start shifted by one first; a bed already converted from it, which is what STAR wrappers and the igv.js test fixtures ship, is passed in as is.

Columns chrom (or chr), start and end are required. score and strand are used when present. The per-junction attributes motif, uniquely_mapped, multi_mapped, maximum_spliced_alignment_overhang and annotated_junction are packed into the bed name column, which is where the track reads its filters and labels from; supply the ones you want to filter or label on. A name column, if you have already packed it yourself, is written through untouched.

Without uniquely_mapped or an explicit score the arcs all draw at the same thickness: igv.js has nothing to size them by.

Usage

loadSpliceJunctionTrackFromLocalData(
  session,
  id,
  trackName,
  tbl,
  trackHeight = 100,
  displayMode = "COLLAPSED",
  deleteTracksOfSameName = TRUE,
  trackConfig = list()
)

Arguments

session

an environment or list, provided and managed by shiny

id

character string, the html element id of this widget instance

trackName

character string

tbl

data.frame, with at least "chrom" "start" "end" columns, in bed coordinates: a 0-based start and an exclusive end

trackHeight

an integer, 100 (pixels) by default

displayMode

character, "COLLAPSED", "EXPANDED" or "SQUISHED"

deleteTracksOfSameName

logical, default TRUE

trackConfig

a named list of additional igv.js track configuration options, the junction ones among them; see loadSpliceJunctionTrackFromURL

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "showcase", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}