loadGFF3TrackFromURL: load a GFF3 track which, with index, is served up by http

In paul-shannon/igvShiny: igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

load a GFF3 track which, with index, is served up by http

Description

load a remote GFF3 track

Usage

loadGFF3TrackFromURL(
  session,
  id,
  trackName,
  gff3URL,
  indexURL,
  color = "gray",
  colorTable,
  colorByAttribute,
  displayMode,
  trackHeight = 50,
  visibilityWindow,
  deleteTracksOfSameName = TRUE
)

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
gff3URL	character string http url for the bam file, typically very large
indexURL	character string http url for the bam file index, typically small
color	character #RGB or a recognized color name. ignored if colorTable and colorByAttribute provided
colorTable	list, mapping a gff3 attribute, typically biotype, to a color
colorByAttribute	character, name of a gff3 attribute in column 9, typically "biotype"
displayMode	character, "EXPANDED", "SQUISHED" or "COLLAPSED"
trackHeight	numeric defaults to 50
visibilityWindow	numeric, Maximum window size in base pairs for which indexed annotations or variants are displayed
deleteTracksOfSameName	logical, default TRUE

Value

nothing

Examples

library(igvShiny)
demo_app_file <-
  system.file(package = "igvShiny", "demos", "igvShinyDemo-GFF3.R")
if (interactive()) {
  shiny::runApp(demo_app_file)
}

paul-shannon/igvShiny documentation built on Aug. 31, 2024, 9:32 a.m.