qtl: plot.cross – R documentation

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plot.cross

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

Examples

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

qtl

Tools for Analyzing QTL Experiments

v1.48-1

GPL-3

Authors

Karl W Broman <broman@wisc.edu> and Hao Wu, with ideas from Gary Churchill and Saunak Sen and contributions from Danny Arends, Robert Corty, Timothee Flutre, Ritsert Jansen, Pjotr Prins, Lars Ronnegard, Rohan Shah, Laura Shannon, Quoc Tran, Aaron Wolen, Brian Yandell, and R Core Team

Initial release

2021-03-24