makeRectangleOverlay {GenomeGraphs}R Documentation

Create a rectangular overlay

Description

Construct ractangular overlays.

Usage

makeRectangleOverlay(start, end, region = NULL, coords = c("genomic", "absolute"), dp = NULL)

Arguments

start Start position in coords coordinates
end End position in coords coordinates
region Which tracks to span, or the y (vertical range)
coords Which coordinate system to use, if absolute then the range is from 0,1 and region become the y coordinates
dp The display parameters

Details

The rectangular overlay can be used to plot overlays in either genomic or absolute coordinates. If coordinates are absolute then the region argument becomes the y arguments.

Value

An object of class RectangleOverlay

Examples

data("exampleData", package = "GenomeGraphs")
cop <- makeGenericArray(intensity  = cn, probeStart = probestart, 
                        dp = DisplayPars(size=3, color = "seagreen", type="dot"))
gdPlot(list(makeGenomeAxis(), cop), overlays =
       makeRectangleOverlay(start = 180350000, end = 180350000 + 1e5, dp = DisplayPars(alpha = .3)))

[Package GenomeGraphs version 1.2.3 Index]