plot the tracks

A function to plot the data for given range

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)