load a splice junction track served up by http

load splice junctions from a BED file reachable by URL, as written by STAR (SJ.out.tab converted to BED). Six columns, with the per-junction attributes packed into the name column as key=value pairs separated by semicolons: motif, uniquely_mapped, multi_mapped, maximum_spliced_alignment_overhang and annotated_junction. The track reads its filters and labels from those attributes.

igv.js draws junctions from a file of that shape only - it derives none of them from a bam file, and it has no sashimi plot. Show this track above a coverage track (bigWig, bedGraph) for the same sample to get the arcs-over-coverage view sashimi plots are wanted for.

Usage

loadSpliceJunctionTrackFromURL(
  session,
  id,
  trackName,
  url,
  indexURL = "",
  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

url

character string http url for the bed file of junctions

indexURL

character string http url for a tabix index, needed only for a bgzipped bed; "" by default, which loads the file whole

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 are read straight off it: minUniquelyMappedReads, minTotalReads, maxFractionMultiMappedReads, minSplicedAlignmentOverhang, thicknessBasedOn, bounceHeightBasedOn, colorBy, labelWith, hideAnnotatedJunctions, hideUnannotatedJunctions, hideMotifs among them.

Value

nothing

Examples

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