TrackData Constructors

In TnT: Interactive Visualization for Genomic Features

suppressPackageStartupMessages({
    library(GenomicFeatures)
    library(TxDb.Hsapiens.UCSC.hg19.knownGene)
})
expose_all <- function (package) {
    attachname <- paste0(package, "_all")
    while (attachname %in% search()) detach(attachname, character.only = TRUE)
    pkgns <- loadNamespace(package)
    attach(pkgns, name = attachname)
    invisible(pkgns)
}
suppressMessages(expose_all("TnT"))

RangeTrackData

data <- RangeTrackData(range = IRanges::IRanges(1:4, 5:8),
                       tooltip = data.frame(start = 1:4, width = 5))
compileTrackData(data)
compileTrackData(data, full = TRUE)

PosTrackData and PosValTrackData

gpos <- GRanges("chr12", IRanges(seq(1, 10, 3), width = 1))
mcols(gpos) <- as.data.frame(gpos)
pt <- PosTrackData(gpos)
compileTrackData(pt)
compileTrackData(pt, full = TRUE)
pt <- PosValTrackData(gpos, val = start(gpos))
compileTrackData(pt)
compileTrackData(pt, full = TRUE)

GeneTrackData

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
gene <- genes(txdb, columns = c("gene_id", "tx_id"))
GeneTrackData(gene[1:4])
ir <- IRanges(1:3, width = 10)
GeneTrackData(ir, labels = paste("gene", 1:3))

GeneTrack (FeatureTrack) from GRanges

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
gr <- genes(txdb)
ft <- FeatureTrack(gr)
#compileTrack(ft)
TnTBoard(ft, GRanges("chr12", IRanges(100000,400000)))

GeneTrackDataFromTxDb

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
GeneTrackDataFromTxDb(txdb, c("chrX", "chrY"))

TxTrackDataFromGRangesList

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
grl <- exonsBy(txdb)[1:3]
a <- TxTrackDataFromGRangesList(grl)
a[1]$key
# When one of the GRanges is empty
grl$`1` <- grl$`1`[numeric(0)]
b <- TxTrackDataFromGRangesList(grl)
b[1]$key
compileTrackData(b)

TxTrack (GroupFeatureTrack) from GRangesList

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
seqlevels(txdb) <- "chrY"
exby <- exonsBy(txdb)
seqlevels(txdb) <- seqlevels0(txdb)

names(exby) <- paste("tx", names(exby))
gft <- GroupFeatureTrack(exby)
TnTBoard(gft, view.range = GRanges("chrY", IRanges(1000, 400000)))

TxTrackDataFromTxDb

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene
tdata <- TxTrackDataFromTxDb(txdb, "chrUn_gl000221")
compileTrackData(tdata)

Misc-tooltip

bt <- BlockTrack(GRanges("chr12", IRanges(1:5 * 100, width = 10), label = paste("range", 1:5)))
trackData(bt)
tooltip(bt)
testthat::expect_error(
    tooltip(bt) <- c(1:5)
)
tooltip(bt) <- data.frame(start = 1:5 * 100)

bt
compileTrack(bt)
TnTBoard(list(bt), view.range = range(trackData(bt)))

Session Info

sessionInfo()

TnT documentation built on Nov. 8, 2020, 8:11 p.m.