% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/igvShiny.R
\name{loadSpliceJunctionTrackFromURL}
\alias{loadSpliceJunctionTrackFromURL}
\title{load a splice junction track served up by http}
\usage{
loadSpliceJunctionTrackFromURL(
  session,
  id,
  trackName,
  url,
  indexURL = "",
  trackHeight = 100,
  displayMode = "COLLAPSED",
  deleteTracksOfSameName = TRUE,
  trackConfig = list()
)
}
\arguments{
\item{session}{an environment or list, provided and managed by shiny}

\item{id}{character string, the html element id of this widget instance}

\item{trackName}{character string}

\item{url}{character string http url for the bed file of junctions}

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

\item{trackHeight}{an integer, 100 (pixels) by default}

\item{displayMode}{character, "COLLAPSED", "EXPANDED" or "SQUISHED"}

\item{deleteTracksOfSameName}{logical, default TRUE}

\item{trackConfig}{a named list of additional igv.js track configuration
options. The junction ones are read straight off it:
\code{minUniquelyMappedReads}, \code{minTotalReads},
\code{maxFractionMultiMappedReads}, \code{minSplicedAlignmentOverhang},
\code{thicknessBasedOn}, \code{bounceHeightBasedOn}, \code{colorBy},
\code{labelWith}, \code{hideAnnotatedJunctions},
\code{hideUnannotatedJunctions}, \code{hideMotifs} among them.}
}
\value{
nothing
}
\description{
load splice junctions from a BED file reachable by URL, as
written by STAR (\code{SJ.out.tab} converted to BED). Six columns, with the
per-junction attributes packed into the name column as \code{key=value}
pairs separated by semicolons: \code{motif}, \code{uniquely_mapped},
\code{multi_mapped}, \code{maximum_spliced_alignment_overhang} and
\code{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.
}
\examples{
library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "showcase", "igvShinyDemo.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

}
\keyword{track_loaders}
