GdObject-class {Gviz} | R Documentation

## GdObject class and methods

### Description

The virtual parent class for all track items in the Gviz package. This class definition contains all the common entities that are needed for a track to be plotted. During object instantiation for any of the sub-classes inheriting from `GdObject`, this class' global ininitializer has to be called in order to assure that all necessary settings are present.

### Objects from the class

A virtual class: No objects may be created from it.

### Slots

`dp`:

  Object of class `DisplayPars`, the display settings controlling the look and feel of a track. See `settings` for details on setting graphical parameters for tracks.

`name`:

  Object of class `"character"`, a human-readable name for the track that will be used in the track's annotation panel if necessary.

`imageMap`:

  Object of class `ImageMap`, containing optional information for an HTML image map. This will be created by the `drawGD` methods when the track is plotted to a device and is usually not set by the user.

### Methods

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

Exported in the name space:

displayPars

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

  Examples:

    `getPar(obj)`

displayPars<-

  `signature(x="GdObject", 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="GdObject", value="character")`: set the single display parameter `name` to `value`. Note that display parameters in the `GdObject` 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="GdObject", value="list")`: set display parameters by the values of the named list in `value`. Note that display parameters in the `GdObject` 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))`

group

  `signature(GdObject="GdObject")`: return grouping information for the individual items in the track. Unless overwritten in one of the sub-classes, this usualy returns `NULL`.

  Usage:

  `group(GdObject)`

  Examples:

    `group(obj)`

names

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

  Usage:

  `names(x)`

  Examples:

    `names(obj)`

names<-

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

  Usage:

  `names<-(x, value)`

  Examples:

    `names(obj) <- "foo"`

coords

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

  Usage:

  `coords(ImageMap)`

  Examples:

    `coords(obj)`

tags

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

  Usage:

  `tags(x)`

  Examples:

    `tags(obj)`

subset

  `signature(x="GdObject")`: subset a `GdObject` by coordinates. Most of the respective sub-classes inheriting from `GdObject` overwrite this method, the default is to return the unaltered input object.

  Usage:

  `subset(x, ...)`

  Additional Arguments:

    `...`: all further arguments are ignored.

  Examples:

    `subset(obj)`

Internal methods:

drawAxis

  `signature(GdObject="GdObject")`: add a y-axis to the title panel of a track if necessary. Unless overwritten in one of the sub-classes this usualy does not plot anything and returns `NULL`.

  Usage:

  `drawAxis(x, ...)`

  Additional Arguments:

    `...`: all further arguments are ignored.

  Examples:

    `Gviz:::drawAxis(obj)`

drawGrid

  `signature(GdObject="GdObject")`: superpose a grid on top of a track if necessary. Unless overwritten in one of the sub-classes this usualy does not plot anything and returns `NULL`.

  Usage:

  `drawGrid(GdObject, ...)`

  Additional Arguments:

    `...`: additional arguments are ignored.

  Examples:

    `Gviz:::drawGrid(obj)`

initialize

  `signature(.Object="GdObject")`: initialize the object. This involves setting up a new environment for the display parameters and filling it up with the current settings. All arguments that have not been clobbered up by one of the sub-class initializers are considered to be additional display parameters and are also added to the environment. See `settings` for details on setting graphical parameters for tracks.

### Display Parameters

The following display parameters are set for objects of class `GdObject` upon instantiation, unless one or more of them have already been set by one of the optional sub-class initializers, which always get precedence over these global defaults. See `settings` for details on setting graphical parameters for tracks.

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

  `alpha.title=NULL`: Numeric scalar. The transparency for the title panel.

  `background.legend="transparent"`: Integer or character scalar. The background color for the legend.

  `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 panel.

  `cex=1`: Numeric scalar. The overall font expansion factor for all text and glyphs, unless a more specific definition exists.

  `cex.axis=NULL`: Numeric scalar. The expansion factor for the axis annotation. Defaults to `NULL`, in which case it is automatically determined 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.border.title="white"`: Integer or character scalar. The border color for the title panels.

  `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 `DataTrack`s 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"` `(Aliases: fontcolor.title)`: Integer or character scalar. The border color for the title panels

  `collapse=TRUE`: Boolean controlling whether 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, unless a more specific definition exists.

  `fontface=1`: Integer or character scalar. The font face for all text, unless a more specific definition exists.

  `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, unless a more specific definition exists.

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

  `fontsize=12`: Numeric scalar. The font size for all text, unless a more specific definition exists.

  `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, unless a more specific definition exists.

  `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 `DataTrack`s 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.border.title=1`: Integer scalar. The border width for the title panels.

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

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

  `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.

  `reverseStrand=FALSE`: Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if `TRUE`. This will effectively mirror the plot on the vertical axis.

  `rotation=0`: The rotation angle for all text unless a more specific definiton exists.

  `rotation.title=90` `(Aliases: rotation.title)`: The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.

  `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.

  `...`: additional display parameters are allowed. Those typically take the value of a valid R color descriptors. The parameter names will later be matched to optional track item types as defined in the 'feature' range attribute, and all tracks of the matched types are colored accordingly. See the documentation of the `GeneRegionTrack` and `AnnotationTrack` classes as well as `grouping` for details.

### Author(s)

Florian Hahne

### See Also

`AnnotationTrack`

`DisplayPars`

`GeneRegionTrack`

`ImageMap`

`collapsing`

`DataTrack`

`grouping`

`panel.grid`

`plotTracks`

`settings`

### Examples

    ## This is a refernce class therefore we show below
    ## an example from AnnotationTrack

    ## An empty object
    AnnotationTrack()

    ## Construct from individual arguments
    st <- c(2000000, 2070000, 2100000, 2160000)
    ed <- c(2050000, 2130000, 2150000, 2170000)
    str <- c("-", "+", "-", "-")
    gr <- c("Group1","Group2","Group1", "Group3")

    annTrack <- AnnotationTrack(start=st, end=ed, strand=str, chromosome=7,
                                genome="hg19", feature="test", group=gr,
                                id=paste("annTrack item", 1:4),
                                name="generic annotation", stacking="squish")

    ## Plotting
    plotTracks(annTrack)

[Package Gviz version 1.36.2 Index]