trackStyle-class: Class '"trackStyle"'

In jianhong/trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data

Class "trackStyle"

Description

An object of class "trackStyle" represents track style.

An object of class "track" represents scores of a given track.

Usage

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

## S4 method for signature 'track'
seqlevelsStyle(x)

## S4 replacement method for signature 'track'
seqlevelsStyle(x) <- value

## S4 method for signature 'track'
show(object)

## S4 method for signature 'track'
x$name

## S4 replacement method for signature 'track'
x$name <- value

setTrackStyleParam(ts, attr, value)

## S4 method for signature 'track,character'
setTrackStyleParam(ts, attr, value)

setTrackXscaleParam(ts, attr, value)

## S4 method for signature 'track,character'
setTrackXscaleParam(ts, attr, value)

setTrackYaxisParam(ts, attr, value)

## S4 method for signature 'track,character'
setTrackYaxisParam(ts, attr, value)

Arguments

x	an object of trackStyle or track
value	values to be assigned.
object	an object of trackStyle.
name	slot name of trackStyle or track
ts	An object of track.
attr	the name of slot of trackStyle object to be changed.

Details

The attr of setTrackXscaleParam could not only be a slot of xscale, but also be position. If the attr is set to position, value must be a list of x, y and label. For example setTrackXscaleParam(track, attr="position", value=list(x=122929675, y=4, label=500))

Slots

tracktype

"character" track type, could be peak, line, histogram, or annotation. Default is "peak". "annotation" is used to mark the peak regions. For interaction data, it could be "heatmap" or "link".

color

"character" track color. If the track has dat and dat2 slot, it should have two values.

NAcolor

"character" NA color for interactionData.

breaks

"numeric" breaks for color keys of interactionData.

height

"numeric" track height. It should be a value between 0 and 1

marginTop

"numeric" track top margin

marginBottom

"numeric" track bottom margin

xscale

object of xscale, describe the details of x-scale

yaxis

object of yaxisStyle, describe the details of y-axis

ylim

"numeric" y-axis range

ylabpos

"character", ylable postion, ylabpos should be 'left', 'right', 'topleft', 'bottomleft', 'topright', 'bottomright', 'abovebaseline', 'underbaseline', or 'none'. For gene type track, it also could be 'upstream' or 'downstream'

ylablas

"numeric" y lable direction. It should be a integer 0-3. See par:las

ylabgp

A "list" object, It will convert to an object of class gpar. This is basically a list of graphical parameter settings of y-label.

ysplit

A "numeric" to split y plot region for interaction data. Default is 0.5, which will split the region half to half. It will only work for back to back plot.

dat

Object of class GRanges the scores of a given track. It should contain score metadata.

dat2

Object of class GRanges the scores of a given track. It should contain score metadata. When dat2 and dat is paired, dat will be drawn as positive value where dat2 will be drawn as negative value (-1 * score)

type

The type of track. It could be 'data', 'gene', 'transcript', 'scSeq', 'lollipopData' or 'interactionData'.

format

The format of the input. It could be "BED", "bedGraph", "WIG", "BigWig" or "BAM"

style

Object of class trackStyle

name

unused yet

See Also

Please try to use importScore and importBam to generate the object.

Examples

extdata <- system.file("extdata", package="trackViewer",
mustWork=TRUE)
fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED")
setTrackStyleParam(fox2, "color", c("red","green"))
setTrackXscaleParam(fox2, "gp", list(cex=.5))
setTrackYaxisParam(fox2, "gp", list(col="blue"))
fox2$dat <- GRanges(score=numeric(0))

jianhong/trackViewer documentation built on Dec. 10, 2024, 10:33 a.m.