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

RangeTrack-class

R Documentation

RangeTrack class and methods

Description

The virtual parent class for all track items in the Gviz package that contain some form of genomic ranges (start, end, strand, chromosome and the associated genome.)

Usage

## S4 method for signature 'RangeTrack'
initialize(.Object, range, chromosome, genome, ...)

## S4 method for signature 'RangeTrack'
ranges(x)

## S4 method for signature 'RangeTrack'
range(x)

## S4 method for signature 'RangeTrack'
seqnames(x)

## S4 method for signature 'RangeTrack'
seqlevels(x)

## S4 method for signature 'RangeTrack'
seqinfo(x)

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

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

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

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

## S4 method for signature 'RangeTrack'
start(x)

## S4 replacement method for signature 'RangeTrack'
start(x) <- value

## S4 method for signature 'RangeTrack'
end(x)

## S4 replacement method for signature 'RangeTrack'
end(x) <- value

## S4 method for signature 'RangeTrack'
width(x)

## S4 replacement method for signature 'RangeTrack'
width(x) <- value

## S4 method for signature 'RangeTrack'
min(x)

## S4 method for signature 'RangeTrack'
max(x)

## S4 method for signature 'RangeTrack'
length(x)

## S4 method for signature 'RangeTrack'
strand(x)

## S4 replacement method for signature 'RangeTrack,ANY'
strand(x) <- value

## S4 method for signature 'RangeTrack'
position(GdObject, from = NULL, to = NULL, sort = FALSE, ...)

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

## S4 method for signature 'RangeTrack'
subset(
  x,
  from = NULL,
  to = NULL,
  sort = FALSE,
  drop = TRUE,
  use.defaults = TRUE,
  ...
)

## S4 method for signature 'RangeTrack,ANY'
split(x, f, drop = FALSE, ...)

## S4 method for signature 'RangeTrack'
values(x)

## S4 method for signature 'RangeTrack'
feature(GdObject)

## S4 replacement method for signature 'RangeTrack,character'
feature(GdObject) <- value

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

Arguments

`.Object`	.Object
`range`	range
`chromosome`	the currently active chromosome which may have to be set for a `RangeTrack` or a `SequenceTrack` object parameters
`genome`	genome
`...`	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.
`GdObject`	the input track object
`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`.
`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).
`use.defaults`	`logical`.
`f`	`factor` in the sense that `as.factor(f)` defines the grouping,

Value

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

Functions

initialize(RangeTrack): Initialize.
ranges(RangeTrack): return the genomic coordinates for the track along with all additional annotation information as an object of class GRanges.
range(RangeTrack): return the genomic coordinates for the track as an object of class IRanges.
seqnames(RangeTrack): return the track's seqnames.
seqlevels(RangeTrack): return the track's seqlevels.
seqinfo(RangeTrack): return the track's seqinfo.
genome(RangeTrack): return the track's genome.
genome(RangeTrack) <- value: set the track's genome. Usually this has to be a valid UCSC identifier, however this is not formally enforced here.
chromosome(RangeTrack): return the chromosome for which the track is defined.
chromosome(RangeTrack) <- 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.
start(RangeTrack): the start of the track items in genomic coordinates.
start(RangeTrack) <- value: replace the start of the track items in genomic coordinates.
end(RangeTrack): the end of the track items in genomic coordinates.
end(RangeTrack) <- value: replace the end of the track items in genomic coordinates.
width(RangeTrack): the width of the track items in genomic coordinates.
width(RangeTrack) <- value: replace the width of the track items in genomic coordinates.
min(RangeTrack): return the start position for the leftmost range item.
max(RangeTrack): return the end position for the rightmost range item.
length(RangeTrack): return the number of items in the track.
strand(RangeTrack): 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.
strand(x = RangeTrack) <- value: replace the strand information for the track items. The replacement value needs to be an appropriate scalar or vector of strand values.
position(RangeTrack): the arithmetic mean of the track item's coordionates, i.e., (end(obj)-start(obj))/2.
x[i: subset the items in the RangeTrack 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(RangeTrack): subset a RangeTrack by coordinates and sort if necessary.
split(x = RangeTrack, f = ANY): split a RangeTrack 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 RangeTrack.
values(RangeTrack): return all additional annotation information except for the genomic coordinates for the track items as a data.frame.
feature(RangeTrack): return the grouping information for track items. For certain sub-classes, groups may be indicated by different colour schemes when plotting. See grouping or AnnotationTrack and GeneRegionTrack for details. @export
feature(GdObject = RangeTrack) <- value: 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 RangeTrack. See grouping or AnnotationTrack and GeneRegionTrack for details. @export
consolidateTrack(RangeTrack): Consolidate.

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.

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.