R: Plot various features of a cross object

plot.cross {qtl} | R Documentation

## Plot various features of a cross object

### Description

Plots grid of the missing genotypes, genetic map, and histograms or barplots of phenotypes for the data from an experimental cross.

### Usage

    ## S3 method for class 'cross'
    plot(x, auto.layout=TRUE, pheno.col,
              alternate.chrid=TRUE, ...)

### Arguments

`x` | An object of class `cross`. See `read.cross` for details.
`auto.layout` | If TRUE, `par(mfrow)` is set so that all plots fit within one figure.
`pheno.col` | Vector of numbers or character strings corresponding to phenotypes that should be plotted. If unspecified, all phenotypes are plotted.
`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

Calls `plotMissing`, `plotMap` and `plotPheno` to plot the missing genotypes, genetic map, and histograms or barplots of all phenotypes.

If `auto.format=TRUE`, `par(mfrow)` is used with `ceiling(sqrt(n.phe+2))` rows and the minimum number of columns so that all plots fit on the plotting device.

Numeric phenotypes are displayed as histograms or barplots by calling `plotPheno`.

### Value

None.

### Author(s)

Karl W Broman, broman@wisc.edu; Brian Yandell

### See Also

`plotMissing`, `plotMap`, `plotPheno`

### Examples

    data(fake.bc)
    plot(fake.bc)

[Package qtl version 1.46-2 Index]