RangeTrack-class {Gviz} | 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.

### Objects from the class

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

### Slots

`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 usualy 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.

`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 `"GdObject"`, directly.

### Methods

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

Exported in the name space:

[

  `signature(x="RangeTrack", i="ANY", j="ANY", drop="ANY")`: 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.

  Additional Arguments:

    `i`, `j`: subsetting indices, `j` is ignored.

    `drop`: argument is ignored.

  Examples:

    `obj[1:5]`

chromosome

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

  Usage:

  `chromosome(GdObject)`

  Examples:

    `chromosome(obj)`

chromosome<-

  `signature(GdObject="RangeTrack")`: 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="RangeTrack")`: 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="RangeTrack")`: 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="RangeTrack")`: 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="RangeTrack")`: 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="RangeTrack", 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 `RangeTrack`. 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="RangeTrack")`: return the track's genome.

  Usage:

  `genome(x)`

  Examples:

    `genome(obj)`

genome<-

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

  Usage:

  `length(x)`

  Examples:

    `length(obj)`

range

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

  Usage:

  `range(x)`

  Examples:

    `range(obj)`

ranges

  `signature(x="RangeTrack")`: 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="RangeTrack")`: 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`.

  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="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.

  Usage:

  `strand(x)`

  Examples:

    `strand(obj)`

strand<-

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

  Usage:

  `values(x)`

  Examples:

    `values(obj)`

min

  `signature(...="RangeTrack")`: return the start position for the leftmost range item.

  Examples:

    `min(obj)`

max

  `signature(...="RangeTrack")`: return the end position for the rightmost range item.

  Examples:

    `max(obj)`

coerce

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

  Examples:

    `as(obj, "data.frame")`

subset

  `signature(x="RangeTrack")`: subset a `RangeTrack` 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)`

Internal methods:

initialize

  `signature(.Object="RangeTrack")`: initialize the object.

Inherited methods:

displayPars

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

  Examples:

    `getPar(obj)`

displayPars<-

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

  Usage:

  `names(x)`

  Examples:

    `names(obj)`

names<-

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

  Usage:

  `names<-(x, value)`

  Examples:

    `names(obj) <- "foo"`

coords

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

  Usage:

  `coords(ImageMap)`

  Examples:

    `coords(obj)`

tags

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

  Usage:

  `tags(x)`

  Examples:

    `tags(obj)`

drawAxis

  `signature(GdObject="RangeTrack")`: add a y-axis to the title panel of a track if necessary. Unless overwritten in one of the sub-classes this usualy does not plot anything and returns `NULL`.

  Usage:

  `drawAxis(x, ...)`

  Additional Arguments:

    `...`: all further arguments are ignored.

  Examples:

    `Gviz:::drawAxis(obj)`

drawGrid

  `signature(GdObject="RangeTrack")`: superpose a grid on top of a track if necessary. Unless overwritten in one of the sub-classes this usualy does not plot anything and returns `NULL`.

  Usage:

  `drawGrid(GdObject, ...)`

  Additional Arguments:

    `...`: additional arguments are ignored.

  Examples:

    `Gviz:::drawGrid(obj)`

### Display Parameters

No formal display parameters are defined for objects of class `RangeTrack`.

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 `RangeTrack` 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 `DataTrack`s 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 `DataTrack`s 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 `DataTrack`s 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`

`DataTrack`

`DisplayPars`

`GdObject`

`GeneRegionTrack`

`GRanges`

`ImageMap`

`IRanges`

`collapsing`

`grouping`

`panel.grid`

`plotTracks`

`settings`

[Package Gviz version 1.24.0 Index]