intensity.plots {DOQTL} | R Documentation

## 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.
`s` | 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.

### Author(s)

Daniel Gatti

### Examples

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

[Package DOQTL version 1.16.2 Index]