load a cram file sitting on the same machine as the shiny app

load a local cram track. Unlike loadBamTrackFromLocalData this loader takes file paths, not an R object: no bioconductor package parses cram, so the file and its index are handed to igv.js untouched, through the directory shiny serves as "tracks".

Usage

loadCramTrackFromLocalData(
  session,
  id,
  trackName,
  cramFile,
  indexFile = paste0(cramFile, ".crai"),
  deleteTracksOfSameName = TRUE,
  trackConfig = list(),
  validateReference = TRUE,
  trackHeight = NULL
)

loadCramTrackFromLocalFile(
  session,
  id,
  trackName,
  cramFile,
  indexFile = paste0(cramFile, ".crai"),
  deleteTracksOfSameName = TRUE,
  trackConfig = list(),
  validateReference = TRUE,
  trackHeight = NULL
)

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

cramFile

character string, path to a cram file

indexFile

character string, path to its crai index, by default the cram file with ".crai" appended

deleteTracksOfSameName

logical, default TRUE

trackConfig

a named list of additional igv.js track configuration options, sort among them; see loadBamTrackFromURL.

validateReference

logical flag, default TRUE: checks track contigs against the active reference genome and emits warnings/toasts on mismatch.

trackHeight

numeric, track height in pixels (default: NULL, igv.js defaults to 300)

Value

nothing

Examples

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