OverlayTrack-class: OverlayTrack class and methods

In Gviz: Plotting data and annotation information along genomic coordinates

Description

A container for other track objects from the Gviz package that allows for overlays of their content on the same region of the plot.

Usage

OverlayTrack(trackList=list(), name="OverlayTrack", ...)

Arguments

trackList	A list of Gviz track objects that all have to inherit from class GdObject.
name	Character scalar of the track's name. This is not really used and only exists fro completeness.
...	All additional parameters are ignored.

Details

A track to conceptionally group other Gviz track objects into a meta track in order to merge them into a single overlay visualization. Only the first track in the supplied list will be inferred when setting up the track title and axis, for all the other tracks only the panel content is plotted.

Value

The return value of the constructor function is a new object of class OverlayTrack.

Objects from the Class

Objects can be created using the constructor function OverlayTrack.

Slots

trackList:

Object of class "list", holding the subtrack objects.

dp:

Object of class DisplayPars, inherited from class GdObject

name:

Object of class "character", inherited from class GdObject

imageMap:

Object of class ImageMap, inherited from class GdObject

Extends

Class "GdObject", directly.

Methods

In the following code chunks, obj is considered to be an object of class OverlayTrack.

Internal methods:

setStacks

signature(GdObject="OverlayTrack"): recompute the stacks based on the available space and on the object's track items and stacking settings. This really just calls the setStacks methods for the contained tracks and only exists for dispatching reasons.

Usage:

setStacks(GdObject, ...)

Examples:

Gviz:::setStacks(obj)

initialize

signature(.Object="OverlayTrack"): initialize the object.

length

signature(x="OverlayTrack"): return the number of items in the track.

Usage:

length(x)

Examples:

length(obj)

subset

signature(x="OverlayTrack"): subset all the contained tracks in an OverlayTrack by coordinates and sort if necessary.

Usage:

subset(x, ...)

Additional Arguments:

...: additional arguments are passed on to the next methods.

Examples:

subset(obj)

Inherited methods:

displayPars

signature(x="OverlayTrack", name="character"): list the value of the display parameter name. See settings for details on display parameters and customization.

Usage:

displayPars(x, name)

Examples:

displayPars(obj, "col")

displayPars

signature(x="OverlayTrack", name="missing"): list the value of all available display parameters. See settings for details on display parameters and customization.

Examples:

displayPars(obj)

getPar

signature(x="OverlayTrack", name="character"): alias for the displayPars method. See settings for details on display parameters and customization.

Usage:

getPar(x, name)

Examples:

getPar(obj, "col")

getPar

signature(x="OverlayTrack", name="missing"): alias for the displayPars method. See settings for details on display parameters and customization.

Examples:

getPar(obj)

displayPars<-

signature(x="OverlayTrack", value="list"): set display parameters using the values of the named list in value. See settings for details on display parameters and customization.

Usage:

displayPars<-(x, value)

Examples:

displayPars(obj) <- list(col="red", lwd=2)

setPar

signature(x="OverlayTrack", value="character"): set the single display parameter name to value. Note that display parameters in the OverlayTrack class are pass-by-reference, so no re-assignmnet to the symbol obj is necessary. See settings for details on display parameters and customization.

Usage:

setPar(x, name, value)

Additional Arguments:

name: the name of the display parameter to set.

Examples:

setPar(obj, "col", "red")

setPar

signature(x="OverlayTrack", value="list"): set display parameters by the values of the named list in value. Note that display parameters in the OverlayTrack class are pass-by-reference, so no re-assignmnet to the symbol obj is necessary. See settings for details on display parameters and customization.

Examples:

setPar(obj, list(col="red", lwd=2))

names

signature(x="OverlayTrack"): return the value of the name slot.

Usage:

names(x)

Examples:

names(obj)

names<-

signature(x="OverlayTrack", value="character"): set the value of the name slot.

Usage:

names<-(x, value)

Examples:

names(obj) <- "foo"

coords

signature(ImageMap="OverlayTrack"): return the coordinates from the internal image map.

Usage:

coords(ImageMap)

Examples:

coords(obj)

tags

signature(x="OverlayTrack"): return the tags from the internal image map.

Usage:

tags(x)

Examples:

tags(obj)

Display Parameters

No formal display parameters are defined for objects of class OverlayTrack.

Additional display parameters are being inherited from the respective parent classes. Note that not all of them may have an effect on the plotting of OverlayTrack objects.

GdObject:

alpha=1: Numeric scalar. The transparency for all track items.

background.panel="transparent": Integer or character scalar. The background color of the content panel.

background.title="lightgray": Integer or character scalar. The background color for the title panels.

col.border.title="transparent": Integer or character scalar. The border color for the title panels.

lwd.border.title=1: Integer scalar. The border width for the title panels.

cex=1: Numeric scalar. The overall font expansion factor for all text.

cex.axis=NULL: Numeric scalar. The expansion factor for the axis annotation. Defaults to NULL, in which case it is computed based on the available space.

cex.title=NULL: Numeric scalar. The expansion factor for the title panel. This effects the fontsize of both the title and the axis, if any. Defaults to NULL, which means that the text size is automatically adjusted to the available space.

col="#0080FF": Integer or character scalar. Default line color setting for all plotting elements, unless there is a more specific control defined elsewhere.

col.axis="white": Integer or character scalar. The font and line color for the y axis, if any.

col.frame="lightgray": Integer or character scalar. The line color used for the panel frame, if frame==TRUE

col.grid="#808080": Integer or character scalar. Default line color for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.

col.line=NULL: Integer or character scalar. Default colors for plot lines. Usually the same as the global col parameter.

col.symbol=NULL: Integer or character scalar. Default colors for plot symbols. Usually the same as the global col parameter.

col.title="white": Integer or character scalar. The font color for the title panels.

collapse=TRUE: Boolean controlling wether to collapse the content of the track to accomodate the minimum current device resolution. See collapsing for details.

fill="lightgray": Integer or character scalar. Default fill color setting for all plotting elements, unless there is a more specific control defined elsewhere.

fontcolor="black": Integer or character scalar. The font color for all text.

fontface=1: Integer or character scalar. The font face for all text.

fontface.title=2: Integer or character scalar. The font face for the title panels.

fontfamily="sans": Integer or character scalar. The font family for all text.

fontfamily.title="sans": Integer or character scalar. The font family for the title panels.

fontsize=12: Numeric scalar. The font size for all text.

frame=FALSE: Boolean. Draw a frame around the track when plotting.

grid=FALSE: Boolean, switching on/off the plotting of a grid.

h=-1: Integer scalar. Parameter controlling the number of horizontal grid lines, see panel.grid for details.

lineheight=1: Numeric scalar. The font line height for all text.

lty="solid": Numeric scalar. Default line type setting for all plotting elements, unless there is a more specific control defined elsewhere.

lty.grid="solid": Integer or character scalar. Default line type for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.

lwd=1: Numeric scalar. Default line width setting for all plotting elements, unless there is a more specific control defined elsewhere.

lwd.grid=1: Numeric scalar. Default line width for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.

min.distance=1: Numeric scalar. The minimum pixel distance before collapsing range items, only if collapse==TRUE. See collapsing for details.

min.height=3: Numeric scalar. The minimum range height in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See collapsing for details.

min.width=1: Numeric scalar. The minimum range width in pixels to display. All ranges are expanded to this size in order to avoid rendering issues. See collapsing for details.

showAxis=TRUE: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).

showTitle=TRUE: Boolean controlling whether to plot a title panel. Although this can be set individually for each track, in multi-track plots as created by plotTracks there will still be an empty placeholder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background color could be set to transparent in order to completely hide it.

size=1: Numeric scalar. The relative size of the track. Can be overridden in the plotTracks function.

v=-1: Integer scalar. Parameter controlling the number of vertical grid lines, see panel.grid for details.

Author(s)

Florian Hahne

See Also

DisplayPars

GdObject

GRanges

HighlightTrack

ImageMap

IRanges

RangeTrack

collapsing

DataTrack

grouping

panel.grid

plotTracks

settings

Examples

## Object construction:
set.seed(123)
dat <- runif(100, min=-2, max=22)
dt1 <- DataTrack(data=dat, start=sort(sample(200, 100)), width=1, genome="hg19")
dt2 <- DataTrack(data=dat, start=sort(sample(200, 100)), width=1, genome="hg19")
ot <- OverlayTrack(trackList=list(dt1, dt2))

Gviz documentation built on March 16, 2021, 6:01 p.m.