GdObject class and methods

Source: R/GdObject-class.R

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 initializer has to be called in order to assure that all necessary settings are present.

# S4 method for class 'GdObject'
initialize(.Object, name, ...)

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

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

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

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

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

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

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

# S4 method for class 'GdObject'
coords(ImageMap)

# S4 method for class 'GdObject'
tags(ImageMap)

# S4 method for class 'GdObject'
subset(x, ...)

# S4 method for class 'GdObject'
names(x)

# S4 method for class 'GdObject,character'
names(x) <- value

group(object) <- value

# S4 method for class 'GdObject'
group(object)

imageMap(GdObject, ...)

# S4 method for class 'GdObject'
imageMap(GdObject)

imageMap(GdObject) <- value

# S4 method for class 'GdObject,ImageMapOrNULL'
imageMap(GdObject) <- value

drawAxis(GdObject, ...)

# S4 method for class 'GdObject'
drawAxis(GdObject, ...)

drawGrid(GdObject, ...)

# S4 method for class 'GdObject'
drawGrid(GdObject, ...)

drawGD(GdObject, ...)

gene(GdObject, ...)

gene(GdObject) <- value

symbol(GdObject, ...)

symbol(GdObject) <- value

transcript(GdObject, ...)

transcript(GdObject) <- value

exon(GdObject, ...)

exon(GdObject) <- value

feature(GdObject, ...)

feature(GdObject) <- value

identifier(GdObject, ...)

identifier(GdObject) <- value

chromosome(GdObject, ...)

# S4 method for class 'GdObject'
chromosome(GdObject)

chromosome(GdObject) <- value

# S4 method for class 'GdObject'
chromosome(GdObject) <- value

position(GdObject, ...)

# S4 method for class 'GdObject'
genome(x)

# S4 method for class 'GdObject'
genome(x) <- value

consolidateTrack(GdObject, ...)

# S4 method for class 'GdObject'
consolidateTrack(GdObject, alpha, ...)

stacking(GdObject, ...)

stacking(GdObject) <- value

stacks(GdObject, ...)

setStacks(GdObject, ...)

# S4 method for class 'GdObject'
setStacks(GdObject, ...)

setCoverage(GdObject, ...)

Arguments

name

Name of the retrieved parameter.

...

Additional arguments.

x

A valid track object class name, or the object itself, in which case the class is derived directly from it.

value

Value to be set.

interactive

logical. Emit the message explaining that setPar no longer supports pass-by-reference semantics and that its result has to be reassigned.

recursive

logical. For composite tracks, also set the display parameters on each of the contained sub-tracks.

asIs

logical. Return the queried parameters as a list. When FALSE, the default, the result of a single-parameter query is unlisted for convenience.

hideInternal

logical. Omit the internal display parameters, i.e., those whose names are prefixed with .__.

ImageMap

Object of class ImageMap, containing optional information for an HTML image map.

GdObject

Object of class GdObject.

Value

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

Details

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 affects the font size 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 objects and when the 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 fontcolour.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 accommodate 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.

  • fontcolour="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 objects and when the 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 objects and when the 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: Numeric scalar. The rotation angle for all text unless a more specific definition exists.

  • rotation.title=90: (Aliases rotation.title) Numeric scalar. 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 your 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 place holder in case any of the other tracks include a title. The same holds true for axes. Note that 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 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.

Functions

  • initialize(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.

  • setPar(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-assignment to the symbol obj is necessary. See settings for details on display parameters and customization.

  • setPar(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-assignment to the symbol obj is necessary. See settings for details on display parameters and customization.

  • displayPars(x = GdObject) <- value: set display parameters using the values of the named list in value. See settings for details on display parameters and customization.

  • getPar(x = GdObject, name = character): Return the value of the display parameter name, delegating to the object's DisplayPars slot. displayPars is a more descriptive alias for this method. See settings for details on display parameters and customization.

  • getPar(x = GdObject, name = missing): Return all display parameters, delegating to the object's DisplayPars slot. displayPars is a more descriptive alias for this method. See settings for details on display parameters and customization.

  • displayPars(x = GdObject, name = character): list the value of the display parameter name. See settings for details on display parameters and customization.

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

  • coords(GdObject): return the coordinates from the internal image map.

  • tags(GdObject): return the tags from the internal image map.

  • subset(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.

  • names(GdObject): return the value of the name slot.

  • names(x = GdObject) <- value: set the value of the name slot.

  • group(object) <- value: Generics for group<-.

  • group(GdObject): return grouping information for the individual items in the track. Unless overwritten in one of the sub-classes, this usually returns NULL.

  • imageMap(): Generics for imageMap.

  • imageMap(GdObject): Extract the content of the imageMap slot.

  • imageMap(GdObject) <- value: Generics for imageMap<-.

  • imageMap(GdObject = GdObject) <- value: Replace the content of the imageMap slot.

  • drawAxis(): Generics for drawAxis.

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

  • drawGrid(): Generics for drawGrid.

  • drawGrid(GdObject): superpose a grid on top of a track if necessary. Unless overwritten in one of the sub-classes this usually does not plot anything and returns NULL.

  • drawGD(): Generics for drawGD.

  • gene(): Generics for gene.

  • gene(GdObject) <- value: Generics for gene<-.

  • symbol(): Generics for symbol.

  • symbol(GdObject) <- value: Generics for symbol<-.

  • transcript(): Generics for transcript.

  • transcript(GdObject) <- value: Generics for transcript<-.

  • exon(): Generics for exon.

  • exon(GdObject) <- value: Generics for exon<-.

  • feature(): Generics for feature.

  • feature(GdObject) <- value: Generics for feature<-.

  • identifier(): Generics for identifier.

  • identifier(GdObject) <- value: Generics for identifier<-.

  • chromosome(): Generics for chromosome.

  • chromosome(GdObject): return the chromosome for which the track is defined.

  • chromosome(GdObject) <- value: Generics for chromosome.

  • chromosome(GdObject) <- value: replace the value of the track's chromosome. This has to be a valid UCSC chromosome identifier or an integer or character scalar that can be reasonably coerced into one.

  • position(): Generics for position.

  • genome(GdObject): return the track's genome.

  • genome(GdObject) <- value: set the track's genome. Usually this has to be a valid UCSC identifier, however this is not formally enforced here.

  • consolidateTrack(): Generics for consolidateTrack.

  • consolidateTrack(GdObject): Determine whether there is alpha settings or not, and add this information as the internal display parameter .__hasAlphaSupport.

  • stacking(): Generics for stacking.

  • stacking(GdObject) <- value: Generics for stacking<-.

  • stacks(): Generics for stacks.

  • setStacks(): Generics for setStacks.

  • setStacks(GdObject): set stacks.

  • setCoverage(): Generics for setCoverage.

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.

Author

Florian Hahne

Examples

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

## An empty object
AnnotationTrack()
#> AnnotationTrack 'AnnotationTrack'
#> | genome: NA
#> | active chromosome: chrNA
#> | annotation features: 0

## 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)