R: Plot grid of missing genotypes

plotMissing {qtl} | R Documentation

## Plot grid of missing genotypes

### Description

Plot a grid showing which genotypes are missing.

### Usage

    plotMissing(x, chr, reorder=FALSE, main="Missing genotypes",
                 alternate.chrid=FALSE, ...)

### Arguments

`x` | An object of class `cross`. See `read.cross` for details.
`chr` | Optional vector indicating the chromosomes to 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.
`...` | Ignored at this point.

### Details

Uses `image` to plot a grid with black pixels where the genotypes are missing. For intercross and 4-way cross data, gray pixels are plotted for the partially missing genotypes (for example, "not AA").

### Value

None.

### Author(s)

Karl W Broman, kbroman@biostat.wisc.edu

### See Also

`plot.cross`, `geno.image`, `image`

### Examples

    data(fake.f2)
    plotMissing(fake.f2)

[Package qtl version 1.41-6 Index]