R: Plot grid of genotype data

geno.image {qtl} | R Documentation

## Plot grid of genotype data

### Description

Plot a grid showing which the genotype data in a cross.

### Usage

    geno.image(x, chr, reorder=FALSE, main="Genotype data",
               alternate.chrid=FALSE, ...)

### Arguments

`x` | An object of class `cross`. See `read.cross` for details.
`chr` | Optional vector indicating the chromosomes to be drawn in the plot. This should be a vector of character strings referring to chromosomes by name; numeric values are converted to strings. Refer to chromosomes with a preceding `-` to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.
`reorder` | Specify whether to reorder individuals according to their phenotypes.
FALSE | Don't reorder
TRUE | Reorder according to the sum of the phenotypes
n | Reorder according to phenotype n
`main` | Title to place on plot.
`alternate.chrid` | If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.
`...` | Passed to `image`.

### Details

Uses `image` to plot a grid with the genotype data. The genotypes AA, AB, BB are displayed in the colors red, blue, and green, respectively. In an intercross, if there are genotypes "not BB" and "not AA", these are displayed in purple and orange, respectively. White pixels indicate missing data.

### Value

None.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`plot.cross`, `plotMissing`, `plotGeno`, `image`

### Examples

    data(listeria)
    geno.image(listeria)

[Package qtl version 1.41-6 Index]