GraphTrackLine-class {rtracklayer} | R Documentation

## Class "GraphTrackLine"

### Description

A UCSC track line for graphical tracks.

### Objects from the Class

Objects can be created by calls of the form `new("GraphTrackLine", ...)` or parsed from a character vector track line with `as(text, "GraphTrackLine")` or converted from a `BasicTrackLine` using `as(basic, "GraphTrackLine")`.

### Slots

`altColor`:

  Object of class `"integer"` giving an alternate color, as from `col2rgb`.

`autoScale`:

  Object of class `"logical"` indicating whether to automatically scale to min/max of the data.

`alwaysZero`:

  Object of class `"logical"` indicating whether to fix the lower limit of the Y axis at zero.

`gridDefault`:

  Object of class `"logical"` indicating whether a grid should be drawn.

`maxHeightPixels`:

  Object of class `"numeric"` of length three (max, default, min), giving the allowable range for the vertical height of the graph.

`graphType`:

  Object of class `"character"`, specifying the graph type, either "bar" or "points".

`viewLimits`:

  Object of class `"numeric"` and of length two specifying the data range (min, max) shown in the graph.

`yLineMark`:

  Object of class `"numeric"` giving the position of a horizontal line.

`yLineOnOff`:

  Object of class `"logical"` indicating whether the `yLineMark` should be visible.

`windowingFunction`:

  Object of class `"character"`, one of "maximum", "mean", "minimum", for removing points when the graph shrinks.

`smoothingWindow`:

  Object of class `"numeric"` giving the window size of a smoother to pass over the graph.

`type`:

  Scalar `"character"` indicating the type of the track, either `"wig"` or `"bedGraph"`.

`name`:

  Object of class `"character"` specifying the name of the track.

`description`:

  Object of class `"character"` describing the track.

`visibility`:

  Object of class `"character"` indicating the default visible mode of the track, see `UCSCTrackModes`.

`color`:

  Object of class `"integer"` representing the track color (as from `col2rgb`).

`priority`:

  Object of class `"numeric"` specifying the rank of this track.

### Extends

Class `"TrackLine"`, directly.

### Methods

as(object, "character")

  Export line to its string representation.

as(object, `"BasicTrackLine"`)

  Convert this line to a basic UCSC track line, using defaults for slots not held in common.

### Author(s)

Michael Lawrence

### References

Official documentation: http://genome.ucsc.edu/goldenPath/help/wiggle.html.

### See Also

`export.wig`, `export.bedGraph` for exporting graphical tracks.

[Package rtracklayer version 1.52.1 Index]