viewTracks: plot the tracks

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

Description

A function to plot the data for given range

Usage

viewTracks(
  trackList,
  chromosome,
  start,
  end,
  strand,
  gr = GRanges(),
  ignore.strand = TRUE,
  viewerStyle = trackViewerStyle(),
  autoOptimizeStyle = FALSE,
  newpage = TRUE,
  operator = NULL,
  smooth = FALSE
)

Arguments

trackList	an object of trackList
chromosome	chromosome
start	start position
end	end position
strand	strand
gr	an object of GRanges
ignore.strand	ignore the strand or not when do filter. default TRUE
viewerStyle	an object of trackViewerStyle
autoOptimizeStyle	should use optimizeStyle to optimize style
newpage	should be draw on a new page?
operator	operator, could be +, -, *, /, ^, %%. "-" means dat - dat2, and so on.
smooth	logical(1) or numeric(1). Smooth the curve or not. If it is numeric, eg n, mean of nearby n points will be used for plot.

Value

An object of viewport for addGuideLine

See Also

See Also as addGuideLine, addArrowMark

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})
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), strand="-")
viewTracks(trackList(track=tracks, fox2=fox2), gr=gr, autoOptimizeStyle=TRUE)

trackViewer documentation built on Feb. 11, 2021, 2 a.m.