GenomeAxisTrack class and methods

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Description

A class representing a customizable genomic axis.

Usage

1
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.

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.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 DataTracks 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 DataTracks and when display parameter grid==TRUE.

lwd.grid=1: Numeric scalar. Default line width for grid lines, both when type=="g" in DataTracks 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

GdObject

GRanges

ImageMap

IRanges

RangeTrack

StackedTrack

collapsing

DataTrack

grouping

panel.grid

plotTracks

settings

Examples

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## 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")))

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