DisplayPars: A class to control the plotting parameters for GdObjects

Source: R/DisplayPars-class.R

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

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 explicitly 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 environment needs to be re-instantiated.

Objects can be created using the constructor function DisplayPars.

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

DisplayPars(...)

getPar(x, name, ...)

# S4 method for class 'DisplayPars,character'
getPar(x, name, asIs = FALSE)

# S4 method for class 'DisplayPars,missing'
getPar(x, hideInternal = TRUE)

displayPars(x, name, ...)

# S4 method for class 'DisplayPars,missing'
displayPars(x, hideInternal = TRUE)

# S4 method for class 'DisplayPars,character'
displayPars(x, name)

# S4 method for class 'DisplayPars'
as.list(x)

setPar(x, value, ...)

# S4 method for class 'DisplayPars,list'
setPar(x, value, interactive = TRUE)

# S4 method for class 'DisplayPars,character'
setPar(x, name, value, interactive = TRUE)

displayPars(x, recursive = FALSE) <- value

# S4 method for class 'DisplayPars,list'
displayPars(x, recursive = FALSE) <- value

# S4 method for class 'DisplayPars'
show(object)

# S4 method for class 'InferredDisplayPars'
as.list(x)

# S4 method for class 'InferredDisplayPars'
show(object)

availableDisplayPars(class)

Arguments

...

All named arguments are stored in the object's environment as individual parameters, regardless of their type.

x

object to set the displayPar value on

name

Name of the retrieved parameter.

asIs

logical

hideInternal

logical

value

named value to be set

interactive

logical

recursive

logical

object

object

class

Either character scalar or object. Supported classes are: GdObject, GenomeAxisTrack, RangeTrack, NumericTrack, DataTrack, IdeogramTrack, StackedTrack, AnnotationTrack, DetailsAnnotationTrack, GeneRegionTrack, BiomartGeneRegionTrack, AlignmentsTrack, SequenceTrack, SequenceBSgenomeTrack, SequenceDNAStringSetTrack, SequenceRNAStringSetTrack

Value

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

availableDisplayPars returns a list of the default display parameters.

Functions

  • DisplayPars(): Constructor function.

  • getPar(): Generics for getPar.

  • getPar(x = DisplayPars, name = character): Alias for the displayPars method.

  • getPar(x = DisplayPars, name = missing): Alias for the displayPars method.

  • displayPars(): Generics for displayPars.

  • displayPars(x = DisplayPars, name = missing): Returns all available display parameters.

  • displayPars(x = DisplayPars, name = character): Returns the value of a subset of display parameters, as identified by name.

  • as.list(DisplayPars): Converts DisplayPars to list.

  • setPar(): Generics for SetPar.

    SetPar generic function

  • setPar(x = DisplayPars, value = list): Sets 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-assignment to the symbol obj is necessary.

  • setPar(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-assignment to the symbol obj is necessary.

  • displayPars(x, recursive = FALSE) <- value: Generics for displayPars<-.

  • displayPars(x = DisplayPars) <- value: Replaces or adds display parameters as provided by the named list items.

  • show(DisplayPars): Show method.

  • as.list(InferredDisplayPars): Return InferredDisplayPars as a list.

  • show(InferredDisplayPars): Show method.

  • availableDisplayPars(): Get default display parameters.

Slots

pars

an environment or a list containing parameter key value pairs.

Author

Florian Hahne

Examples

## Construct object
dp <- DisplayPars(col = "red", lwd = 2, transformation = log2)
dp
#> Display parameters:
#> col = red 
#> lwd = 2 
#> transformation = function (x)  .Primitive("log2")

## Query parameters
displayPars(dp)
#> $col
#> [1] "red"
#> 
#> $lwd
#> [1] 2
#> 
#> $transformation
#> function (x)  .Primitive("log2")
#> 
displayPars(dp, "col")
#> [1] "red"
getPar(dp, c("col", "transformation"))
#> $col
#> [1] "red"
#> 
#> $transformation
#> function (x)  .Primitive("log2")
#> 

## Modify parameters
displayPars(dp) <- list(lty = 1, fontsize = 3)
setPar(dp, "pch", 20)
#> Note that the behaviour of the 'setPar' method has changed. You need to reassign the result to an object for the side effects to happen. Pass-by-reference semantic is no longer supported.
#> Display parameters:
#> col = red 
#> fontsize = 3 
#> lty = 1 
#> lwd = 2 
#> pch = 20 
#> transformation = function (x)  .Primitive("log2")
dp
#> Display parameters:
#> col = red 
#> fontsize = 3 
#> lty = 1 
#> lwd = 2 
#> transformation = function (x)  .Primitive("log2")
## Default parameters
availableDisplayPars("GenomeAxisTrack")
#> 
#> The following display parameters are available for 'GenomeAxisTrack' objects:
#> (see ? GenomeAxisTrack for details on their usage)
#> 
#> add35: FALSE 
#> add53: FALSE 
#> alpha (inherited from class 'GdObject'): 1 
#> alpha.title (inherited from class 'GdObject'): NULL
#> background.legend (inherited from class 'GdObject'): transparent 
#> background.panel (inherited from class 'GdObject'): transparent 
#> background.title: transparent 
#> cex: 0.8 
#> cex.axis (inherited from class 'GdObject'): NULL
#> cex.id: 0.7 
#> cex.title (inherited from class 'GdObject'): NULL
#> col: darkgray 
#> col.axis (inherited from class 'GdObject'): white 
#> col.border.title: transparent 
#> col.frame (inherited from class 'GdObject'): lightgray 
#> col.grid (inherited from class 'GdObject'): #808080 
#> col.id: white 
#> col.line (inherited from class 'GdObject'): NULL
#> col.range: cornsilk4 
#> col.symbol (inherited from class 'GdObject'): NULL
#> col.title (inherited from class 'GdObject'): white 
#> collapse (inherited from class 'GdObject'): TRUE 
#> distFromAxis: 1 
#> exponent: NULL
#> fill (inherited from class 'GdObject'): lightgray 
#> fill.range: cornsilk3 
#> fontcolor: #808080 
#> fontcolour (inherited from class 'GdObject'): black 
#> fontface (inherited from class 'GdObject'): 1 
#> fontface.title (inherited from class 'GdObject'): 2 
#> fontfamily (inherited from class 'GdObject'): sans 
#> fontfamily.title (inherited from class 'GdObject'): sans 
#> fontsize: 10 
#> frame (inherited from class 'GdObject'): FALSE 
#> grid (inherited from class 'GdObject'): FALSE 
#> h (inherited from class 'GdObject'): -1 
#> labelPos: alternating 
#> lineheight (inherited from class 'GdObject'): 1 
#> littleTicks: FALSE 
#> lty (inherited from class 'GdObject'): solid 
#> lty.grid (inherited from class 'GdObject'): solid 
#> lwd: 2 
#> lwd.border.title: 1 
#> lwd.grid (inherited from class 'GdObject'): 1 
#> lwd.title (inherited from class 'GdObject'): 1 
#> min.distance (inherited from class 'GdObject'): 1 
#> min.height (inherited from class 'GdObject'): 3 
#> min.width (inherited from class 'GdObject'): 1 
#> reverseStrand (inherited from class 'GdObject'): FALSE 
#> rotation (inherited from class 'GdObject'): 0 
#> rotation.title (inherited from class 'GdObject'): 90 
#> scale: NULL
#> showAxis (inherited from class 'GdObject'): TRUE 
#> showId: FALSE 
#> showTitle: FALSE 
#> size: NULL
#> ticksAt: NULL
#> v (inherited from class 'GdObject'): -1