browseTracks: browse tracks

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

browse tracks

Description

browse tracks by a web browser.

Usage

browseTracks(
  trackList,
  gr = GRanges(),
  ignore.strand = TRUE,
  width = NULL,
  height = NULL,
  ...
)

Arguments

trackList	an object of trackList
gr	an object of GRanges
ignore.strand	ignore the strand or not when do filter. default TRUE
width	width of the figure
height	height of the figure
...	parameters not used

Value

An object of class htmlwidget that will intelligently print itself into HTML in a variety of contexts including the R console, within R Markdown documents, and within Shiny output bindings.

Examples

extdata <- system.file("extdata", package="trackViewer", mustWork=TRUE)
files <- dir(extdata, "-.wig")
tracks <- lapply(paste(extdata, files, sep="/"), 
                 importScore, format="WIG")
tracks <- lapply(tracks, function(.ele) {strand(.ele@dat) <- "-"; .ele})
names(tracks) <- c("trackA", "trackB")
fox2 <- importScore(paste(extdata, "fox2.bed", sep="/"), format="BED")
dat <- coverageGR(fox2@dat)
fox2@dat <- dat[strand(dat)=="+"]
fox2@dat2 <- dat[strand(dat)=="-"]
gr <- GRanges("chr11", IRanges(122929275, 122930122))
browseTracks(trackList(tracks, fox2), gr=gr)

jianhong/trackViewer documentation built on Nov. 10, 2024, 10:33 a.m.