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)

### 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.

### Value

An object of `viewport` for `addGuideLine`

### Author(s)

Jianhong Ou

### 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 1.14.1 Index]