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Edit File: mqmplotmultitrait.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 the results from a genomescan using a multiple-QTL model...</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.multitrait {qtl}"><tr><td>mqmplot.multitrait {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot the results from a genomescan using a multiple-QTL model on multiple phenotypes</h2> <h3>Description</h3> <p>Plotting routine to display the results from a multiple-QTL model on multiple phenotypes. It supports four different visualizations: a contourmap, heatmap, 3D graph or a multiple QTL plot created by using <code><a href="plot.scanone.html">plot.scanone</a></code> on the <code>mqmmulti</code> object </p> <h3>Usage</h3> <pre> mqmplot.multitrait(result, type=c("lines","image","contour","3Dplot"), group=NULL, meanprofile=c("none","mean","median"), theta=30, phi=15, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>result</code></td> <td> <p> Result object from <code><a href="mqmscanall.html">mqmscanall</a></code> </p> </td></tr> <tr valign="top"><td><code>type</code></td> <td> <p> Selection of the plot method to visualize the data: "lines" (defaut plotting option), "image", "contour" and "3Dplot" </p> </td></tr> <tr valign="top"><td><code>group</code></td> <td> <p> A numeric vector indicating which traits to plot. NULL means no grouping </p> </td></tr> <tr valign="top"><td><code>meanprofile</code></td> <td> <p> Plot a mean/median profile from the group selected </p> </td></tr> <tr valign="top"><td><code>theta</code></td> <td> <p> Horizontal axis rotation in a 3D plot </p> </td></tr> <tr valign="top"><td><code>phi</code></td> <td> <p> Vertical axis rotation in a 3D plot </p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Additional arguments passed to <code><a href="../../graphics/html/plot.html">plot</a></code>.</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.multitrait(result,"lines") mqmplot.multitrait(result,"contour") mqmplot.multitrait(result,"image") mqmplot.multitrait(result,"3Dplot") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>