R, Bioconductor, Gviz

  • R : free software environment for statistical computing and graphics.
  • Bioconductor: R packages for bioinformatics.
  • Gviz: Package for genomic region visualization.

Example

Important functions

  • IdeogramTrack: Chromosome ideogram
  • GenomeAxisTrack: An axis
  • GeneRegionTrack: Same but for genes
  • AnnotationTrack: Ranges annotation

  • DataTrack: Different types of graphs

  • plotTracks merges different tracks.

Simple example

## Let's say we have 'cnv' and 'qtls' GRanges
library(Gviz)
atrack = AnnotationTrack(cnv, name = "CNVs")
gatrack = GenomeAxisTrack()
qtrack = DataTrack(qtls, data = qtls$logPv, name = "QTLs")
plotTracks(list(gatrack, atrack, qtrack))

Data tracks

Data track

qtrack = DataTrack(qtls, data = qtls$logPv, name = "QTLs", 
    type = "h")
plotTracks(qtrack)

Chromosome ideogram and axis

ideoTrack = IdeogramTrack(genome = "hg19", chromosome = "chr21")
gatrack = GenomeAxisTrack()
plotTracks(list(ideoTrack, gatrack, qtrack))

Gene model

I downloaded Gencode annotation and parsed it to look like this

load("gencode.v25.ch21.RData")
gencode[1]
## GRanges object with 1 range and 3 metadata columns:
##       seqnames             ranges strand |        feature
##          <Rle>          <IRanges>  <Rle> |    <character>
##   [1]    chr21 [5011799, 5011874]      + | protein_coding
##              transcript      symbol
##             <character> <character>
##   [1] ENST00000624081.1 CH507-9B2.2
##   -------
##   seqinfo: 25 sequences from an unspecified genome; no seqlengths

Gene model track

from = 36400000
to = 37000000
genetrack = GeneRegionTrack(gencode, genome = "hg19", 
    name = "Gene", transcriptAnnotation = "symbol")
plotTracks(genetrack, from = from, to = to)

Joining the tracks

plotTracks(list(ideoTrack, gatrack, genetrack, qtrack), 
    from = from, to = to)

UCSC tracks

UCSC tracks can be imported directly, but for some reason it's slow.

ucscGenes = UcscTrack(genome = "hg19", chromosome = "chr21", 
    from = min(start(gr)), to = max(end(gr)), track = "knownGene", 
    trackType = "GeneRegionTrack", rstarts = "exonStarts", 
    rends = "exonEnds", gene = "name", symbol = "name", 
    transcript = "name", strand = "strand", fill = "#8282d2", 
    name = "UCSC Genes")
plotTracks(list(gatrack, atrack))

Demo - Custom annotations

  • Color using the feature argument.
  • Group using the group argument.

Other examples - Overlay data

Other examples - Read Alignment

alTrack = AlignmentsTrack(system.file(package = "Gviz", 
    "extdata", "gapped.bam"), isPaired = TRUE)

Other examples - Read Alignment

plotTracks(c(bmt, alTrack), from = afrom + 12700, to = afrom + 
    15200, chromosome = "chr12", type = c("coverage", 
    "sashimi"))

Other examples - Read Alignment

Links