viewTracks {trackViewer} | R Documentation

## 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
    )

### 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)

[Package trackViewer version 1.24.2 Index]