makeRectangleOverlay: Create a rectangular overlay

In GenomeGraphs: Plotting genomic information from Ensembl

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)))

Example output

Loading required package: biomaRt
Loading required package: grid

GenomeGraphs documentation built on Oct. 31, 2019, 4:34 a.m.