EVOLUTION-MANAGER
Edit File: plot.missing.html
<!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 missing genotypes</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 plotMissing {qtl}"><tr><td>plotMissing {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot grid of missing genotypes</h2> <h3>Description</h3> <p>Plot a grid showing which genotypes are missing. </p> <h3>Usage</h3> <pre> plotMissing(x, chr, reorder=FALSE, main="Missing genotypes", alternate.chrid=FALSE, ...) </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 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>...</code></td> <td> <p>Ignored at this point.</p> </td></tr> </table> <h3>Details</h3> <p>Uses <code><a href="../../graphics/html/image.html">image</a></code> 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"). </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="geno.image.html">geno.image</a></code>, <code><a href="../../graphics/html/image.html">image</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) plotMissing(fake.f2) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>