viewTracks: plot the 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

plot the tracks

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,
  lollipop_style_switch_limit = 10
)

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 +, -, *, /, ^, %%, and NA. "-" means dat - dat2, and so on. NA means do not apply any operator. Note: if multiple operator is supplied, please make sure the length of operator keep same as the length of trackList.
smooth	logical(1) or numeric(). Plot smooth curve or not. If it is numeric, eg n, mean of nearby n points will be used for plot. If it is numeric, the second number will be the color. Default coloer is 2 (red).
lollipop_style_switch_limit	The cutoff value for lollipop style for the 'circle' type. If the max score is greater than this cutoff value, trackViewer will only plot one shape at the highest score. Otherwise trackViewer will draw the shapes like 'Tanghulu'.

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)

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