loadGFF3TrackFromLocalData: load a GFF3 track defined by local data

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 defined by local data

Description

load a local GFF3 track file

Usage

loadGFF3TrackFromLocalData(
  session,
  id,
  trackName,
  tbl.gff3,
  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
tbl.gff3	data.frame in standard 9-column GFF3 format
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. 12, 2024, 7:41 p.m.