In Marlin-Na/TnT: Interactive Visualization for Genomic Features

Composite track is a way to combine multiple types of features into one track. A composite track can be constructed by combining a list of different tracks with function merge.

Label, background and height of the composite track will be derived from the component tracks and can be further accessed and modified with trackSpec and trackSpec<-.

suppressPackageStartupMessages({
    library(TnT)
    library(GenomicFeatures)
    library(AnnotationHub)
})
set.seed(42)

Composite a Block Track and a Pin Track

First to construct a block track and a pin track from data.

gr <- GRanges("chr1", IRanges(c(11000, 20000, 60000), width = 2000))
gpos <- GRanges("chr1", IRanges(c(12000, 21000, 61000), width = 1), value = c(1, 2, 3))

btrack <- TnT::BlockTrack(gr, label = "Block Track", tooltip = as.data.frame(gr), color = "lightblue4")
ptrack <- TnT::PinTrack(gpos, label = "Pin Track", tooltip = as.data.frame(gpos), background = "beige")

Then use merge to construct a composite track and showing it.

ctrack <- TnT::merge(btrack, ptrack)
TnTBoard(ctrack)

Be aware that the components in a composite track are rendered according to the order in merge. For example, the block track will cover the pin track if we switch the order.

TnTBoard(merge(ptrack, btrack)) # the pin track has been covered

Show all three tracks and add axis indicator.

TnTGenome(list(ctrack, ptrack, btrack))

Gene Track and CpG Islands

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
gtrack <- TnT::GeneTrackFromTxDb(txdb, label = "Gene", color = "burlywood3")

ah <- AnnotationHub()
ah <- query(ah, "cpgisland")
cpg <- ah[[names(ah[ah$genome == "hg19"])]]
cpgtrack <- TnT::BlockTrack(cpg, label = "CpG Islands", tooltip = as.data.frame(cpg),
                            color = "lightblue")
TnTGenome(merge(cpgtrack, gtrack),
          view.range = GRanges("chr1", IRanges(84884317, 85205497)))