GFF3Track-class: Constructor for GFF3Track

In paul-shannon/igvR: igvR: integrative genomics viewer

Constructor for GFF3Track

Description

GFF3Track creates an IGV track for 9-column gene annotation tables

Usage

GFF3Track(
  trackName,
  tbl.track = data.frame(),
  url = NA_character_,
  indexURL = NA_character_,
  trackColor = "black",
  colorByAttribute = NA_character_,
  colorTable = list(),
  displayMode,
  trackHeight,
  visibilityWindow
)

Arguments

trackName	A character string, used as track label by igv, we recommend unique names per track.
tbl.track	data.frame with 9 columns as defined at http://uswest.ensembl.org/info/website/upload/gff3.html
url	character the web location of a 9-column table, gzipped or not
indexURL	character the matching tabix index file
trackColor	character a recognized color name or RGB triple
colorByAttribute	a name from a column 9 attribute
colorTable	list which maps the colorByAttribute values to different colors
displayMode	"COLLAPSED", "SQUISHED" or "EXPANDED". Spelling and case must be precise.
trackHeight	track height, typically in range 20 (for annotations) and up to 1000 (for large sample vcf files)
visibilityWindow	Maximum window size in base pairs for which indexed annotations or variants are displayed. Defaults: 1 MB for variants, whole chromosome for other track types.

Details

Detailed description goes here

Value

A GFF3Track object

Examples

tbl.gff3 <- read.table(system.file(package="igvR", "extdata", "GRCh38.94.NDUFS2.gff3"),
                       sep="\t", as.is=TRUE)
colnames(tbl.gff3) <- c("seqid", "source", "type", "start", "end", "score", "strand",
                        "phase", "attributes")
colors <- list("antisense" = "blueviolet",
               "protein_coding" = "blue",
               "retained_intron" = "rgb(0, 150, 150)",
               "processed_transcript" = "purple",
               "processed_pseudogene" = "#7fff00",
               "unprocessed_pseudogene" = "#d2691e",
               "default" = "black")
track <- GFF3Track("dataframe gff3", tbl.gff3, colorByAttribute="biotype", colorTable=colors,
                   url=NA_character_, indexURL=NA_character_, displayMode="EXPANDED", trackHeight=200,
                   visibilityWindow=100000)

   # gff3 table structure is not bed-like. find chrom, start, end as seen below

roi <- with(tbl.gff3, sprintf("%s:%d-%d",
                              seqid[1],
                              as.integer(min(start)) - 1000,
                              as.integer(max(end)) + 1000))
if(interactive()){
   igv <- igvR()
   setGenome(igv, "hg38")
   setBrowserWindowTitle(igv, "GWAS demo")
   showGenomicRegion(igv, roi)
   displayTrack(igv, track)
   }

paul-shannon/igvR documentation built on Nov. 17, 2024, 9:36 p.m.