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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: Heatmap of a genome of MQM scan on multiple phenotypes</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 mqmplot.heatmap {qtl}"><tr><td>mqmplot.heatmap {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Heatmap of a genome of MQM scan on multiple phenotypes</h2> <h3>Description</h3> <p>Plotting routine to display a heatmap of results obtained from a multiple-QTL model on multiple phenotypes (the output of <code><a href="mqmscanall.html">mqmscanall</a></code>) </p> <h3>Usage</h3> <pre> mqmplot.heatmap(cross, result, directed=TRUE, legend=FALSE, breaks = c(-100,-10,-3,0,3,10,100), col = c("darkblue","blue","lightblue","yellow","orange","red"), ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>cross</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>result</code></td> <td> <p> Result object from mqmscanall, the object needs to be of class <code>mqmmulti</code> </p> </td></tr> <tr valign="top"><td><code>directed</code></td> <td> <p> Take direction of QTLs into account (takes more time because of QTL direction calculations </p> </td></tr> <tr valign="top"><td><code>legend</code></td> <td> <p> If TRUE, add a legend to the plot </p> </td></tr> <tr valign="top"><td><code>breaks</code></td> <td> <p> Color break points for the LOD scores </p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p> Colors used between breaks </p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Additional arguments passed to the <code><a href="../../graphics/html/image.html">image</a></code> function </p> </td></tr> </table> <h3>Author(s)</h3> <p>Danny Arends <a href="mailto:danny.arends@gmail.com">danny.arends@gmail.com</a> </p> <h3>See Also</h3> <ul> <li><p> The MQM tutorial: <a href="https://rqtl.org/tutorials/MQM-tour.pdf">https://rqtl.org/tutorials/MQM-tour.pdf</a> </p> </li> <li> <p><code><a href="MQM.html">MQM</a></code> - MQM description and references </p> </li> <li> <p><code><a href="mqmscan.html">mqmscan</a></code> - Main MQM single trait analysis </p> </li> <li> <p><code><a href="mqmscanall.html">mqmscanall</a></code> - Parallellized traits analysis </p> </li> <li> <p><code><a href="mqmaugment.html">mqmaugment</a></code> - Augmentation routine for estimating missing data </p> </li> <li> <p><code><a href="mqmautocofactors.html">mqmautocofactors</a></code> - Set cofactors using marker density </p> </li> <li> <p><code><a href="mqmsetcofactors.html">mqmsetcofactors</a></code> - Set cofactors at fixed locations </p> </li> <li> <p><code><a href="mqmpermutation.html">mqmpermutation</a></code> - Estimate significance levels </p> </li> <li> <p><code><a href="scanone.html">scanone</a></code> - Single QTL scanning </p> </li></ul> <h3>Examples</h3> <pre> data(multitrait) multitrait <- fill.geno(multitrait) # impute missing genotype data result <- mqmscanall(multitrait, logtransform=TRUE) mqmplot.heatmap(multitrait,result) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>