GenomeAxisTrack-class {Gviz} | R Documentation

## GenomeAxisTrack class and methods

### Description

A class representing a customizable genomic axis.

### Usage

    GenomeAxisTrack(range=NULL, name="Axis", id, ...)

### Arguments

`range` | Optional `GRanges` or `IRanges` object to highlight certain regions on the axis.
`name` | Character scalar of the track's name used in the title panel when plotting.
`id` | A character vector of the same length as `range` containing identifiers for the ranges. If missing, the constructor will try to extract the ids from `names(range)`.
`...` | Additional items which will all be interpreted as further display parameters. See `settings` and the "Display Parameters" section below for details.

### Details

A `GenomeAxisTrack` can be customized using the familiar display parameters. By providing a `GRanges` or `IRanges` object to the constructor, ranges on the axis can be further highlighted.\

With the `scale` display parameter, a small scale indicator can be shown instead of the entire genomic axis. The scale can either be provided as a fraction of the plotting region (it will be rounded to the nearest human readable absolute value) or as an absolute value and is always displayed in bp, kb, mb or gb units. Note that most display parameters for the `GenomeAxisTrack` are ignored when a scale is used insterad of the full axis. In particular, only the parameters `exponent`, `alpha`, `lwd`, `col`, `cex`, `distFromAxis` and `labelPos` are used.

### Value

The return value of the constructor function is a new object of class `GenomeAxisTrack`.

### Objects from the class

Objects can be created using the constructor function `GenomeAxisTrack`.

### Slots

`range`:

  Object of class `GRanges`, highlighted on the axis.

`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 `GenomeAxisTrack`.

Exported in the name space:

[

  `signature(x="GenomeAxisTrack")`: subset the `GRanges` object in the `range` slot. For most applications, the `subset` method may be more appropriate.

  Additional Arguments:

    `i`: subsetting incides.

  Examples:

    `obj[1:5]`

start, end, width

  `signature(x="GenomeAxisTrack")`: 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)`

range

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

  Usage:

  `range(x)`

  Examples:

    `range(obj)`

ranges

  `signature(x="GenomeAxisTrack")`: 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)`

strand

  `signature(x="GenomeAxisTrack")`: 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)`

values

  `signature(x="GenomeAxisTrack")`: return all additional annotation information except for the genomic coordinates for the track items.

  Usage:

  `values(x)`

  Examples:

    `values(obj)`

subset

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

length

  `signature(x="GenomeAxisTrack")`: return the number of items stored in the `ranges` slot.

  Usage:

  `length(x)`

  Examples:

    `length(obj)`

Internal methods:

drawGD

  `signature(GdObject="GenomeAxisTrack")`: the workhorse function to plot the object.

  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)`

    `Gviz:::drawGD(obj, minBase=1, maxBase=100)`

    `Gviz:::drawGD(obj, prepare=TRUE, subset=FALSE)`

collapseTrack

  `signature(GdObject="GenomeAxisTrack")`: preprocess the track before plotting. This will collapse overlapping track items based on the available resolution and increase the width and height of all track objects to a minimum value to avoid rendering issues. See `collapsing` for details.

  Usage:

  `collapseTrack(GdObject, diff=.pxResolution(coord="x"))`

  Additional Arguments:

    `diff`: the minimum pixel width to display, everything below that will be inflated to a width of `diff`.

  Examples:

    `Gviz:::collapseTrack(obj)`

initialize

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

show

  `signature(object="GenomeAxisTrack")`: show a human-readable summary of the object

Inherited:

displayPars

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

  Examples:

    `getPar(obj)`

displayPars<-

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

  Usage:

  `names(x)`

  Examples:

    `names(obj)`

names<-

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

  Usage:

  `names<-(x, value)`

  Examples:

    `names(obj) <- "foo"`

coords

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

  Usage:

  `coords(ImageMap)`

  Examples:

    `coords(obj)`

tags

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

  Usage:

  `tags(x)`

  Examples:

    `tags(obj)`

drawAxis

  `signature(GdObject="GenomeAxisTrack")`: 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="GenomeAxisTrack")`: 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

The following display parameters are set for objects of class `GenomeAxisTrack` 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.

  `add35=FALSE`: Logical scalar. Add 3' to 5' direction indicators.

  `add53=FALSE`: Logical scalar. Add 5' to 3' direction indicators.

  `background.title="transparent"`: Character scalar. The background color for the title panel. Defaults to omit the background.

  `cex=0.8`: Numeric scalar. The overall font expansion factor for the axis annotation text.

  `cex.id=0.7`: Numeric scalar. The text size for the optional range annotation.

  `col="darkgray"`: Character scalar. The color for the axis lines and tickmarks.

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

  `col.id="white"`: Character scalar. The text color for the optional range annotation.

  `col.range="cornsilk4"`: Character scalar. The border color for highlighted regions on the axis.

  `distFromAxis=1`: Numeric scalar. Control the distance of the axis annotation from the tick marks.

  `exponent=NULL`: Numeric scalar. The exponent for the axis coordinates, e.g., 3 means mb, 6 means gb, etc. The default is to automatically determine the optimal exponent.

  `fill.range="cornsilk3"`: Character scalar. The fill color for highlighted regions on the axis.

  `fontcolor="#808080"`: Character scalar. The font color for the axis annotation text.

  `fontsize=10`: Numeric scalar. Font size for the axis annotation text in points.

  `labelPos="alternating"`: Character vector, one in "alternating", "revAlternating", "above" or "below". The vertical positioning of the axis labels. If `scale` is not `NULL`, the possible values are "above", "below" and "beside".

  `littleTicks=FALSE`: Logical scalar. Add more fine-grained tick marks.

  `lwd=2`: Numeric scalar. The line width for the axis elementes.

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

  `scale=NULL`: Numeric scalar. If not `NULL` a small scale is drawn instead of the full axis, if the value is between 0 and 1 it is interpreted as a fraction of the current plotting region, otherwise as an absolute length value in genomic coordinates.

  `showId=FALSE`: Logical scalar. Show the optional range highlighting annotation.

  `showTitle=FALSE`: Logical scalar. Plot a title panel. Defaults to omit the title panel.

  `size=NULL`: Numeric scalar. The relative size of the track. Can be overridden in the `plotTracks` function. Defaults to the ideal size based on the other track settings.

  `ticksAt=NULL`: Numeric scalar. The exact x-position for tickmarks (in base-pairs).

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 `GenomeAxisTrack` objects.

  `GdObject`:

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

    `alpha.title=NULL`: Numeric scalar. The transparency for the title panel.

    `background.legend="transparent"`: Integer or character scalar. The background color for the legend.

    `background.panel="transparent"`: Integer or character scalar. The background color of the content panel.

    `cex.axis=NULL`: Numeric scalar. The expansion factor for the axis annotation. Defaults to `NULL`, in which case it is automatically determined 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.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"` `(Aliases: fontcolor.title)`: Integer or character scalar. The border color for the title panels

    `collapse=TRUE`: Boolean controlling whether 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.

    `fontface=1`: Integer or character scalar. The font face for all text, unless a more specific definition exists.

    `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, unless a more specific definition exists.

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

    `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, unless a more specific definition exists.

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

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

    `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.

    `reverseStrand=FALSE`: Logical scalar. Set up the plotting coordinates in 3' -> 5' direction if `TRUE`. This will effectively mirror the plot on the vertical axis.

    `rotation=0`: The rotation angle for all text unless a more specific definiton exists.

    `rotation.title=90` `(Aliases: rotation.title)`: The rotation angle for the text in the title panel. Even though this can be adjusted, the automatic resizing of the title panel will currently not work, so use at own risk.

    `showAxis=TRUE`: Boolean controlling whether to plot a y axis (only applies to track types where axes are implemented).

    `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`

`GRanges`

`GdObject`

`IRanges`

`ImageMap`

`RangeTrack`

`StackedTrack`

`DataTrack`

`collapsing`

`grouping`

`panel.grid`

`plotTracks`

`settings`

### Examples

    ## Construct object
    axTrack <- GenomeAxisTrack(name="Axis",
    range <- IRanges(start=c(100, 300, 800), end=c(150, 400, 1000)))

    ## Plotting
    plotTracks(axTrack, from=0, to=1100)

    ## Track names
    names(axTrack)
    names(axTrack) <- "foo"

    ## Subsetting and splitting
    subTrack <- subset(axTrack, from=0, to=500)
    length(subTrack)
    subTrack[1]
    split(axTrack, c(1,1,2))

    ## Accessors
    start(axTrack)
    end(axTrack)
    width(axTrack)

    strand(axTrack)

    range(axTrack)
    ranges(axTrack)

    ## Annotation
    values(axTrack)

    ## Grouping
    group(axTrack)

    ## HTML image map
    coords(axTrack)
    tags(axTrack)
    axTrack <- plotTracks(axTrack)$foo
    coords(axTrack)
    tags(axTrack)

    ## adding an axis to another track
    data(cyp2b10)
    grTrack <- GeneRegionTrack(start=26682683, end=26711643,
    		rstart=cyp2b10$start, rends=cyp2b10$end, chromosome=7, genome="mm9",
    		transcript=cyp2b10$transcript, gene=cyp2b10$gene, symbol=cyp2b10$symbol,
    		name="Cyp2b10", strand=cyp2b10$strand)

    plotTracks(list(grTrack, GenomeAxisTrack()))
    plotTracks(list(grTrack, GenomeAxisTrack(scale=0.1)))
    plotTracks(list(grTrack, GenomeAxisTrack(scale=5000)))
    plotTracks(list(grTrack, GenomeAxisTrack(scale=0.5, labelPos="below")))

[Package Gviz version 1.28.3 Index]