StackedTrack class and methods

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 StackedTrack
initialize(.Object, stacking, ...)

# S4 method for StackedTrack
stacking(GdObject)

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

# S4 method for StackedTrack
stacks(GdObject)

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

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

# S4 method for StackedTrack,ANY,ANY,ANY
[(x, i, j, ..., drop = TRUE)

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

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

Arguments

.Object: .Object
stacking: stacking
...: Additional arguments.
GdObject: Object of GdObject-class.
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 to cannot be larger than from.
sort: logical.
stacks: logical. Set if stacking should be preserved.

Value

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

Functions

initialize(StackedTrack): Initialize.
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): Consolidate. a display parameter)
x[i: 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 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.
range: Object of class GRanges, the genomic ranges of the track items as well as additional annotation information in its elementMetaData slot. Please not 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 name 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 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 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.

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"
)
# \dontshow{
## For some annoying reason the postscript device does not know about
## the sans font
if (!interactive()) {
    font <- ps.options()$family
    displayPars(annTrack) <- list(fontfamily = font, fontfamily.title = font)
}
# }

## Plotting
plotTracks(annTrack)


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