StackedTrack class and methods

Source: R/StackedTrack-class.R

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.

# S4 method for class 'StackedTrack'
initialize(.Object, stacking, ...)

# S4 method for class 'StackedTrack'
stacking(GdObject)

# S4 method for class 'StackedTrack,character'
stacking(GdObject) <- value

# S4 method for class 'StackedTrack'
stacks(GdObject)

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

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

# S4 method for class 'StackedTrack,ANY,ANY,ANY'
x[i, j, ..., drop = TRUE]

# S4 method for class 'StackedTrack'
subset(x, from = NULL, to = NULL, sort = FALSE, stacks = FALSE, ...)

# S4 method for class 'StackedTrack'
drawGD(GdObject, ...)

Arguments

.Object

The object skeleton passed on by new() during class instantiation, to be filled in by the initialize method.

stacking

The stacking type for overlapping items of the track. One of c(hide, dense, squish, pack, full). Currently, only squish (make best use of the available space), dense (no stacking, collapse overlapping ranges), and hide (do not show any track items at all) are implemented.

...

Additional arguments.

GdObject

Object of class GdObject.

value

Value to be set.

x

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

i

Numeric scalar, index to subset.

j

Numeric scalar, index to subset. Ignored.

drop

logical, indicating if levels that do not occur should be dropped (if f is a factor).

from, to

Numeric scalar, giving the range of genomic coordinates to limit the tracks in. Note that from cannot be larger than to.

sort

logical. Sort the track's ranges by their genomic coordinates after subsetting.

stacks

logical. Set if stacking should be preserved.

Value

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

Functions

  • initialize(StackedTrack): Initialize the stacking slot (validating it against the allowed stackingValues) and reset the stacks slot, before deferring to the RangeTrack initializer for the remaining slots.

  • stacking(StackedTrack): return the current stacking type.

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

  • stacks(StackedTrack): return the stack indices for each track item.

  • setStacks(StackedTrack): recompute the stacks based on the available space and on the object's track items and stacking settings.

  • consolidateTrack(StackedTrack): For StackedTrack objects, set the stacking (which could have been passed in as a display parameter) before deferring to the RangeTrack method for the remaining consolidation steps.

  • 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.

  • subset(StackedTrack): subset a StackedTrack by coordinates and sort if necessary.

  • drawGD(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.

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.

range

Object of class GRanges, the genomic ranges of the track items as well as additional annotation information in its elementMetadata slot. Please note that the slot is actually implemented as a class union between GRanges and IRanges to increase efficiency, for instance for DataTrack objects. This usually does not concern the user.

chromosome

Object of class character, the chromosome on which the track is defined. There can only be a single chromosome for one track. For certain subclasses, the space of allowed chromosome names is limited (e.g., only those chromosomes that exist for a particular genome). Throughout the package, chromosome names have to be entered either as a single integer scalar or as a character scalar of the form chrXYZ, where XYZ may be an arbitrary character string.

genome

Object of class character, the genome for which the track is defined. For most sub-classes this has to be a valid UCSC genome identifier, however this may not always be formally checked upon object instantiation.

stacking

Object of class character, the stacking type of overlapping items on the final plot. One of 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.

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)


## Stacking
stacking(annTrack)
#> [1] "squish"
stacking(annTrack) <- "dense"
plotTracks(annTrack)