qtl: plot.missing – R documentation

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qtl

plot.missing

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, broman@wisc.edu

Examples

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

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