GdObject-class: GdObject class and methods
In ivanek/Gviz: Plotting data and annotation information along genomic coordinates

GdObject-class

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

Usage

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

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

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

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

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

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

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

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

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

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

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

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

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

group(GdObject, ...)

group(GdObject) <- value

## S4 method for signature 'GdObject'
group(GdObject)

imageMap(GdObject, ...)

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

imageMap(GdObject) <- value

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

drawAxis(GdObject, ...)

## S4 method for signature 'GdObject'
drawAxis(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 signature 'GdObject'
chromosome(GdObject)

chromosome(GdObject) <- value

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

position(GdObject, ...)

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

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

consolidateTrack(GdObject, ...)

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

stacking(GdObject, ...)

stacking(GdObject) <- value

stacks(GdObject, ...)

setStacks(GdObject, ...)

## S4 method for signature '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`
`recursive`	`logical`
`asIs`	`logical`
`hideInternal`	`logical`
`ImageMap`	Object of `ImageMap-class`, containing optional information for an HTML image map.
`GdObject`	Object of `GdObject-class`.

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 colour for the legend.
background.panel="transparent" Integer or character scalar. The background colour of the content panel.
background.title="lightgray" Integer or character scalar. The background colour 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 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 colour 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 colour for the y axis, if any.
col.border.title="white" Integer or character scalar. The border colour for the title panels.
col.frame="lightgray" Integer or character scalar. The line colour used for the panel frame, if frame==TRUE
col.grid="#808080" Integer or character scalar. Default line colour for grid lines, both when type=="g" in DataTracks and when display parameter grid==TRUE.
col.line=NULL Integer or character scalar. Default colours for plot lines. Usually the same as the global col parameter.
col.symbol=NULL Integer or character scalar. Default colours for plot symbols. Usually the same as the global col parameter.
col.title="white" (Aliases fontcolour.title) Integer or character scalar. The border colour 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 colour setting for all plotting elements, unless there is a more specific control defined elsewhere.
fontcolour="black" Integer or character scalar. The font colour 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 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.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 DataTracks 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 definition 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 place holder in case any of the other tracks include a title. The same holds true for axes. Note that the the title panel background colour 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 colour 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 coloured accordingly. See the documentation of the GeneRegionTrack and AnnotationTrack classes as well as grouping for details.

Value

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

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): alias for the displayPars method. See settings for details on display parameters and customization.
getPar(x = GdObject, name = missing): alias for the displayPars 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(): Generics for group.
group(GdObject) <- 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.
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): Consolidate. 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(GdObject): set stacks.
setCoverage(): Generics for “.

Slots

dp: Object of DisplayPars-class, 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 ImageMap-class, 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(s)

Florian Hahne

Examples

## This is a reference 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)

ivanek/Gviz documentation built on Nov. 20, 2023, 8:16 p.m.