load a bam track which, with index, is served up by http

load a remote bam track

Usage

loadBamTrackFromURL(
  session,
  id,
  trackName,
  bamURL,
  indexURL,
  deleteTracksOfSameName = TRUE,
  displayMode = "EXPANDED",
  showAllBases = FALSE,
  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

bamURL

character string http url for the bam file, typically very large

indexURL

character string http url for the bam file index, typically small

deleteTracksOfSameName

logical, default TRUE

displayMode

character string, possible values are "EXPANDED"(default), "SQUISHED" or "COLLAPSED"

showAllBases

logical, show all bases in the alignment, default FALSE

trackConfig

a named list of additional igv.js track configuration options. Alignment tracks read sort: list(sort = list(chr = "chr1", position = 155160540, option = "TAG", tag = "HP")) sorts the reads at that 1-based position by the HP tag. Any igv.js sort option works (BASE, STRAND, INSERT_SIZE, ...); reads sort descending unless direction = "ASC".

Value

nothing

Examples

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