GenomeGraphs (version 1.32.0)

makeRectangleOverlay: 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

Value

An object of class RectangleOverlay

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.

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)))