intensity.plots: Plot founders and F1 hybrids or genotype state means and variances on an intensity plot.

Description

Given the X and Y (or rho and theta) array intensities, plot the values for one SNP and color and mark the founders and FALSE1s.

Usage

founder.F1.intensity.plot(theta, rho, s = 1, is.founder.F1, plotNew = TRUE, ...) intensity.mean.covar.plot(s, states, theta, rho, r.t.means, r.t.covars, sample, ...)

Arguments

theta

Numeric matrix containing theta (or X) intensity values.

rho

Numeric matrix containing rho (or Y) intensity values.

Numeric integer containing the SNP index in rho and theta to plot.

is.founder.F1

Boolean vector containing TRUE for samples that are DO founders or FALSE1s and FALSEALSE for those that are not.

plotNew

Boolean that is TRUE if a new plot should be made and FALSEALSE if the points should be added to the existing plot.

states

Character vector containing genotypes state letter codes.

r.t.means

Numeric three dimensional array containing genotype state means in rho and theta coordinates.

r.t.covars

Numeric three dimensional array containing genotype state variances in rho and theta coordinates.

sample

Numeric value containing the sample index into the rho and theta matrices to plot in orange.

...

Additional arguments to be passed to plot.

Value

No return value. A scatter plot is made of the rho and theta (or X and Y) intensities at the requested SNP. Founders and F1 hybrid samples are colored.

Examples

Run this code

  ## Not run:  founder.F1.intensity.plot(theta, rho, s = 1, is.founder.F1, plotNew = TRUE, ...)

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