DisplayPars-class {Gviz} | R Documentation

## DisplayPars class and method

### Description

All tracks within this package are highly customizable. The `DisplayPars` class facilitates this and provides a unified API to the customization parameters.

### Usage

    DisplayPars(...)

    availableDisplayPars(class)

### Arguments

`...` | All named arguments are stored in the object's environment as individual parameters, regardless of their type.
`class` | A valid track object class name, or the object itself, in which case the class is derived directly from it.

### Details

The individual parameters in a `DisplayParameters` class are stored as pointers in an environment. This has the upshot of not having to copy the whole track object when changing parameters, and parameters can be updated without the need to explicietly reassign the track to a symbol (i.e., updating of parameters happens in place). The downside is that upon copying of track objects, the parameter emvironment needs to be reinstantiated.

The default display parameters for a track object class can be queried using the `availableDisplayPars` function.

### Value

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

`availableDisplayPars` returns a list of the default display parameters.

### Objects from the Class

Objects can be created using the constructor function `DisplayPars`.

### Slots

`pars`:

  Object of class `"environment"`, the container for all customization parameters.

### Methods

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

Exported in the name space:

displayPars

  `signature(x="DisplayPars", name="character")`: return the value of a subset of display parameters, as identified by `name`.

  Usage:

  `displayPars(x, name)`

  Examples:

    `displayPars(obj, c("foo", "bar"))`

    `displayPars(obj, "foobar")`

displayPars

  `signature(x="DisplayPars", name="missing")`: return all available display parameters.

  Usage:

  `displayPars(x)`

  Examples:

    `displayPars(obj)`

getPar

  `signature(x="DisplayPars", name="character")`: alias for the `displayPars` method.

  Usage:

  `getPar(x, name)`

  Examples:

    `getPar(obj, "col")`

getPar

  `signature(x="DisplayPars", name="missing")`: alias for the `displayPars` method.

  Usage:

  `getPar(x)`

  Examples:

    `getPar(obj)`

displayPars<-

  `signature(x="DisplayPars", value="list")`: replace or add display parameters as provided by the named list items.

  Usage:

  `displayPars<-(x, value)`

  Examples:

    `displayPars(obj) <- list(foo="a", bar=2)`

setPar

  `signature(x="DisplayPars", value="character")`: set the single display parameter `name` to `value`. Note that display parameters in the `DisplayPars` class are pass-by-reference, so no re-assignmnet to the symbol `obj` is necessary.

  Usage:

  `setPar(x, name, value)`

  Additional Arguments:

    `name`: the name of the display parameter to set.

  Examples:

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

setPar

  `signature(x="DisplayPars", value="list")`: set display parameters by the values of the named list in `value`. Note that display parameters in the `DisplayPars` class are pass-by-reference, so no re-assignmnet to the symbol `obj` is necessary.

  Examples:

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

Internal methods:

initialize

  `signature(.Object = "DisplayPars")`: initialize the object.

show

  `signature(object = "DisplayPars")`: show a human-readable summary of the object.

### Author(s)

Florian Hahne

### Examples

    ## Construct object
    dp <- DisplayPars(col="red", lwd=2, transformation=log2)
    dp

    ## Query parameters
    displayPars(dp)
    displayPars(dp, "col")
    getPar(dp, c("col", "transformation"))

    ## Modify parameters
    displayPars(dp) <- list(lty=1, fontsize=3)
    setPar(dp, "pch", 20)
    dp

    ## Default parameters
    availableDisplayPars("GenomeAxisTrack")

[Package Gviz version 1.36.2 Index]