StackedTrack class and methods

Description

The virtual parent class for all track types in the Gviz package which contain potentially overlapping annotation items that have to be stacked when plotted.

Objects from the Class

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

Slots

stacking:

Object of class "character", the stacking type of overlapping items on the final plot. One in c(hide, dense, squish, pack,full). Currently, only hide (do not show the track items at all), squish (make best use of the available space) and dense (no stacking at all) are implemented.

stacks:

Object of class "numeric", holding the stack indices for each track item. This slot is usually populated by calling the setStacks method upon plotting, since the correct stacking is a function of the available plotting space.

range:

Object of class GRanges, inherited from class RangeTrack

chromosome:

Object of class "character", inherited from class RangeTrack

genome:

Object of class "character", inherited from class RangeTrack

dp:

Object of class DisplayPars, inherited from class GdObject

name:

Object of class "character", inherited from class GdObject

imageMap:

Object of class ImageMap, inherited from class GdObject

Extends

Class "RangeTrack", directly.

Class "GdObject", by class "RangeTrack", distance 2.

Methods

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

Exported in the name space:

stacking

signature(GdObject="StackedTrack"): return the current stacking type.

Usage:

stacking(GdObject)

Examples:

stacking(obj)

stacking<-

signature(GdObject="StackedTrack", value="character"): set the object's stacking type to one in c(hide, dense, squish, pack,full).

Usage:

stacking<-(GdObject, value)

Additional Arguments:

value: replacement value.

Examples:

stacking(obj) <- "squish"

Internal methods:

drawGD

signature(GdObject="StackedTrack"): plot the object to a graphics device. The return value of this method is the input object, potentially updated during the plotting operation. Internally, there are two modes in which the method can be called. Either in 'prepare' mode, in which case no plotting is done but the stacking information is updated based on the available space, or in 'plotting' mode, in which case the actual graphical output is created. Note that the method for this particular subclass is usually called through inheritance and not particularly useful on its own.

Usage:

drawGD(GdObject, minBase, maxBase, prepare=FALSE, subset=TRUE, ...)

Additional Arguments:

minBase, maxBase: the coordinate range to plot.

prepare: run method in preparation or in production mode.

subset: subset the object to the visible region or skip the potentially expensive subsetting operation.

...: all further arguments are ignored.

Examples:

Gviz:::drawGD(obj, prepare=FALSE)

setStacks

signature(GdObject="StackedTrack"): recompute the stacks based on the available space and on the object's track items and stacking settings.

Usage:

setStacks(GdObject, from, to)

Additional Arguments:

from, to: compute stacking within a certain coordinates range. This needs to be supplied for the plotting function to know the current genomic coordinates.

Examples:

Gviz:::setStacks(obj)

stacks

signature(GdObject="StackedTrack"): return the stack indices for each track item.

Usage:

stacks(GdObject)

Examples:

Gviz:::stacks(obj)

initialize

signature(.Object="StackedTrack"): initialize the object.

Inherited methods:

[

signature(x="StackedTrack", i="ANY", j="ANY", drop="ANY"): subset the items in the StackedTrack object. This is essentially similar to subsetting of the GRanges object in the range slot. For most applications, the subset method may be more appropriate.

Additional Arguments:

i, j: subsetting indices, j is ignored.

drop: argument is ignored.

Examples:

obj[1:5]

chromosome

signature(GdObject="StackedTrack"): return the chromosome for which the track is defined.

Usage:

chromosome(GdObject)

Examples:

chromosome(obj)

chromosome<-

signature(GdObject="StackedTrack"): 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.

Usage:

chromosome<-(GdObject, value)

Additional Arguments:

value: replacement value.

Examples:

chromosome(obj) <- "chr12"

start, end, width

signature(x="StackedTrack"): the start or end coordinates of the track items, or their width in genomic coordinates.

Usage:

start(x)

end(x)

width(x)

Examples:

start(obj)

end(obj)

width(obj)

start<-, end<-, width<-

signature(x="StackedTrack"): replace the start or end coordinates of the track items, or their width.

Usage:

start<-(x, value)

end<-(x, value)

width<-(x, value)

Additional Arguments:

value: replacement value.

Examples:

start(obj) <- 1:10

end(obj) <- 20:30

width(obj) <- 1

position

signature(GdObject="StackedTrack"): the arithmetic mean of the track item's coordionates, i.e., (end(obj)-start(obj))/2.

Usage:

position(GdObject)

Examples:

position(obj)

feature

signature(GdObject="StackedTrack"): return the grouping information for track items. For certain sub-classes, groups may be indicated by different color schemes when plotting. See grouping or AnnotationTrack and GeneRegionTrack for details.

Usage:

feature(GdObject)

Examples:

feature(obj)

feature<-

signature(gdObject="StackedTrack", value="character"): set the grouping information for track items. This has to be a factor vector (or another type of vector that can be coerced into one) of the same length as the number of items in the StackedTrack. See grouping or AnnotationTrack and GeneRegionTrack for details.

Usage:

feature<-(GdObject, value)

Additional Arguments:

value: replacement value.

Examples:

feature(obj) <- c("a", "a", "b", "c", "a")

genome

signature(x="StackedTrack"): return the track's genome.

Usage:

genome(x)

Examples:

genome(obj)

genome<-

signature(x="StackedTrack"): set the track's genome. Usually this has to be a valid UCSC identifier, however this is not formally enforced here.

Usage:

genome<-(x, value)

Additional Arguments:

value: replacement value.

Examples:

genome(obj) <- "mm9"

length

signature(x="StackedTrack"): return the number of items in the track.

Usage:

length(x)

Examples:

length(obj)

range

signature(x="StackedTrack"): return the genomic coordinates for the track as an object of class IRanges.

Usage:

range(x)

Examples:

range(obj)

ranges

signature(x="StackedTrack"): return the genomic coordinates for the track along with all additional annotation information as an object of class GRanges.

Usage:

ranges(x)

Examples:

ranges(obj)

split

signature(x="StackedTrack"): split a StackedTrack object by an appropriate factor vector (or another vector that can be coerced into one). The output of this operation is a list of objects of the same class as the input object, all inheriting from class StackedTrack.

Usage:

split(x, f, ...)

Additional Arguments:

f: the splitting factor.

...: all further arguments are ignored.

Examples:

split(obj, c("a", "a", "b", "c", "a"))

strand

signature(x="StackedTrack"): return a vector of strand specifiers for all track items, in the form '+' for the Watson strand, '-' for the Crick strand or '*' for either of the two.

Usage:

strand(x)

Examples:

strand(obj)

strand<-

signature(x="StackedTrack"): replace the strand information for the track items. The replacement value needs to be an appropriate scalar or vector of strand values.

Usage:

strand<-(x, value)

Additional Arguments:

value: replacement value.

Examples:

strand(obj) <- "+"

values

signature(x="StackedTrack"): return all additional annotation information except for the genomic coordinates for the track items as a data.frame.

Usage:

values(x)

Examples:

values(obj)

coerce

signature(from="StackedTrack", to="data.frame"): coerce the GRanges object in the range slot into a regular data.frame.

Examples:

as(obj, "data.frame")

subset

signature(x="StackedTrack"): subset a StackedTrack by coordinates and sort if necessary.

Usage:

subset(x, from, to, sort=FALSE, ...)

Additional Arguments:

from, to: the coordinates range to subset to.

sort: sort the object after subsetting. Usually not necessary.

...: additional arguments are ignored.

Examples:

subset(obj, from=10, to=20, sort=TRUE)

displayPars

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

Examples:

getPar(obj)

displayPars<-

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

Usage:

names(x)

Examples:

names(obj)

names<-

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

Usage:

names<-(x, value)

Examples:

names(obj) <- "foo"

coords

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

Usage:

coords(ImageMap)

Examples:

coords(obj)

tags

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

Usage:

tags(x)

Examples:

tags(obj)

Display Parameters

The following display parameters are set for objects of class StackedTrack 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.

reverseStacking=FALSE: Logical flag. Reverse the y-ordering of stacked items. I.e., features that are plotted on the bottom-most stacks will be moved to the top-most stack and vice versa.

stackHeight=0.75: Numeric between 0 and 1. Controls the vertical size and spacing between stacked elements. The number defines the proportion of the total available space for the stack that is used to draw the glyphs. E.g., a value of 0.5 means that half of the available vertical drawing space (for each stacking line) is used for the glyphs, and thus one quarter of the available space each is used for spacing above and below the glyph. Defaults to 0.75.

Additional display parameters are being inherited from the respective parent classes. Note that not all of them may have an effect on the plotting of StackedTrack objects.

GdObject:

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

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 panels.

col.border.title="transparent": Integer or character scalar. The border color for the title panels.

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

cex=1: Numeric scalar. The overall font expansion factor for all text.

cex.axis=NULL: Numeric scalar. The expansion factor for the axis annotation. Defaults to NULL, in which case it is computed 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.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 DataTracks 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": Integer or character scalar. The font color for the title panels.

collapse=TRUE: Boolean controlling wether 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.

fontface=1: Integer or character scalar. The font face for all text.

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.

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

fontsize=12: Numeric scalar. The font size for all text.

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.

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

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.

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.

Author(s)

Florian Hahne

See Also

AnnotationTrack

DisplayPars

GdObject

GeneRegionTrack

GRanges

ImageMap

IRanges

RangeTrack

collapsing

DataTrack

grouping

panel.grid

plotTracks

settings

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