EVOLUTION-MANAGER
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml"><head><title>R: Plot grid of genotype data</title> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> <link rel="stylesheet" type="text/css" href="R.css" /> </head><body> <table width="100%" summary="page for geno.image {qtl}"><tr><td>geno.image {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot grid of genotype data</h2> <h3>Description</h3> <p>Plot a grid showing which the genotype data in a cross. </p> <h3>Usage</h3> <pre> geno.image(x, chr, reorder=FALSE, main="Genotype data", alternate.chrid=FALSE, col=NULL, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>cross</code>. See <code><a href="read.cross.html">read.cross</a></code> for details. </p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>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 <code>-</code> to have all chromosomes but those considered. A logical (TRUE/FALSE) vector may also be used.</p> </td></tr> <tr valign="top"><td><code>reorder</code></td> <td> <p>Specify whether to reorder individuals according to their phenotypes. </p> <table summary="Rd table"> <tr> <td style="text-align: left;"> FALSE </td><td style="text-align: left;"> Don't reorder </td> </tr> <tr> <td style="text-align: left;"> TRUE </td><td style="text-align: left;"> Reorder according to the sum of the phenotypes </td> </tr> <tr> <td style="text-align: left;"> n </td><td style="text-align: left;"> Reorder according to phenotype n</td> </tr> </table> </td></tr> <tr valign="top"><td><code>main</code></td> <td> <p>Title to place on plot.</p> </td></tr> <tr valign="top"><td><code>alternate.chrid</code></td> <td> <p>If TRUE and more than one chromosome is plotted, alternate the placement of chromosome axis labels, so that they may be more easily distinguished.</p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p>Vector of colors. The first is for missing genotypes, followed by colors for each of the genotypes. If <code>NULL</code>, a default set of colors are used.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to <code><a href="../../graphics/html/image.html">image</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>Uses <code><a href="../../graphics/html/image.html">image</a></code> 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. </p> <h3>Value</h3> <p>None.</p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a> </p> <h3>See Also</h3> <p><code><a href="plot.cross.html">plot.cross</a></code>, <code><a href="plot.missing.html">plotMissing</a></code>, <code><a href="plot.geno.html">plotGeno</a></code>, <code><a href="../../graphics/html/image.html">image</a></code> </p> <h3>Examples</h3> <pre> data(listeria) geno.image(listeria) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>