trackStyle-class {trackViewer} | R Documentation

## Class `"trackStyle"`

### Description

An object of class `"trackStyle"` represents track style.

An object of class `"track"` represents scores of a given track.

### Usage

    ## S4 method for signature 'track'
    seqlevels(x)

    ## S4 method for signature 'track'
    seqlevelsStyle(x)

    ## S4 replacement method for signature 'track'
    seqlevelsStyle(x) <- value

    ## S4 method for signature 'track'
    show(object)

    ## S4 method for signature 'track'
    x$name

    ## S4 replacement method for signature 'track'
    x$name <- value

    setTrackStyleParam(ts, attr, value)

    ## S4 method for signature 'track,character'
    setTrackStyleParam(ts, attr, value)

    setTrackXscaleParam(ts, attr, value)

    ## S4 method for signature 'track,character'
    setTrackXscaleParam(ts, attr, value)

    setTrackYaxisParam(ts, attr, value)

    ## S4 method for signature 'track,character'
    setTrackYaxisParam(ts, attr, value)

### Arguments

`x` | an object of trackStyle
`value` | values to be assigned.
`object` | an object of trackStyle.
`name` | slot name of trackStyle
`ts` | An object of `track`.
`attr` | the name of slot of `trackStyle` object to be changed.

### Details

The attr of `setTrackXscaleParam` could not only be a slot of xscale, but also be position. If the attr is set to position, value must be a list of x, y and label. For example setTrackXscaleParam(track, attr="position", value=list(x=122929675, y=4, label=500))

### Slots

`tracktype`

  `"character"` track type, could be peak or cluster. Default is "peak". "cluster" is not supported yet. For interaction data, it could be "heatmap" or "link".

`color`

  `"character"` track color. If the track has dat and dat2 slot, it should have two values.

`NAcolor`

  `"character"` NA color for interactionData.

`breaks`

  `"numeric"` breaks for color keys of interactionData.

`height`

  `"numeric"` track height. It should be a value between 0 and 1

`marginTop`

  `"numeric"` track top margin

`marginBottom`

  `"numeric"` track bottom margin

`xscale`

  object of `xscale`, describe the details of x-scale

`yaxis`

  object of `yaxisStyle`, describe the details of y-axis

`ylim`

  `"numeric"` y-axis range

`ylabpos`

  `"character"`, ylable postion, ylabpos should be 'left', 'right', 'topleft', 'bottomleft', 'topright', 'bottomright', 'abovebaseline' or 'underbaseline'. For gene type track, it also could be 'upstream' or 'downstream'

`ylablas`

  `"numeric"` y lable direction. It should be a integer 0-3. See `par:las`

`ylabgp`

  A `"list"` object, It will convert to an object of class `gpar`. This is basically a list of graphical parameter settings of y-label.

`dat`

  Object of class `GRanges` the scores of a given track. It should contain score metadata.

`dat2`

  Object of class `GRanges` the scores of a given track. It should contain score metadata. When dat2 and dat is paired, dat will be drawn as positive value where dat2 will be drawn as negative value (-1 * score)

`type`

  The type of track. It could be 'data', 'gene', 'transcript', 'scSeq', 'lollipopData' or 'interactionData'.

`format`

  The format of the input. It could be "BED", "bedGraph", "WIG", "BigWig" or "BAM"

`style`

  Object of class `trackStyle`

`name`

  unused yet

### See Also

Please try to use `importScore` and `importBam` to generate the object.

### Examples

    extdata <- system.file("extdata", package="trackViewer",
    mustWork=TRUE)
    fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED")
    setTrackStyleParam(fox2, "color", c("red","green"))
    setTrackXscaleParam(fox2, "gp", list(cex=.5))
    setTrackYaxisParam(fox2, "gp", list(col="blue"))
    fox2$dat <- GRanges(score=numeric(0))

[Package trackViewer version 1.28.1 Index]