EVOLUTION-MANAGER
Edit File: plotModel.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 a 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 plotModel {qtl}"><tr><td>plotModel {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot a QTL model</h2> <h3>Description</h3> <p>Plot a graphical representation of a QTL model, with nodes representing QTL and line segments representing pairwise interactions. </p> <h3>Usage</h3> <pre> plotModel(qtl, formula, circrad.rel=0.25, circrad.abs, cex.name=1, chronly=FALSE, order, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>qtl</code></td> <td> <p>A QTL object (as created by <code><a href="makeqtl.html">makeqtl</a></code>) or vector of character strings indicating the names for the QTL. This is also allowed to be a list that contains a component named <code>"chr"</code> (and, optionally, components names <code>"pos"</code> and <code>"formula"</code>).</p> </td></tr> <tr valign="top"><td><code>formula</code></td> <td> <p>Optional formula defining the QTL model. If missing, we look for an attribute <code>"formula"</code> to the input QTL object or a item named <code>"formula"</code> within the QTL object.</p> </td></tr> <tr valign="top"><td><code>circrad.rel</code></td> <td> <p>Radius of the circles that indicate the QTL, relative to the distance between the circles.</p> </td></tr> <tr valign="top"><td><code>circrad.abs</code></td> <td> <p>Optional radius of the circles that indicate the QTL; note that the plotting region will have x- and y-axis limits spanning 3 units.</p> </td></tr> <tr valign="top"><td><code>cex.name</code></td> <td> <p>Character expansion for the QTL names.</p> </td></tr> <tr valign="top"><td><code>chronly</code></td> <td> <p>If TRUE and a formal QTL object is given, only the chromosome IDs are used to identify the QTL.</p> </td></tr> <tr valign="top"><td><code>order</code></td> <td> <p>Optional vector indicating a permutation of the QTL to define where they are to appear in the plot. QTL are placed around a circle, starting at the top and going clockwise.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to the function <code><a href="../../graphics/html/plot.html">plot</a></code>.</p> </td></tr> </table> <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="stepwiseqtl.html">stepwiseqtl</a></code>, <code><a href="makeqtl.html">makeqtl</a></code> </p> <h3>Examples</h3> <pre> # plot a QTL model, using a vector of character strings to define the QTL plotModel(c("1","4","6","15"), formula=y~Q1+Q2+Q3*Q4) # plot an additive QTL model data(hyper) hyper <- calc.genoprob(hyper) qtl <- makeqtl(hyper, chr=c(1,4,6,15), pos=c(68.3,30,60,18), what="prob") plotModel(qtl) # include an interaction plotModel(qtl, formula=y~Q1+Q2+Q3*Q4) # alternatively, include the formula as an attribute to the QTL object attr(qtl, "formula") <- y~Q1+Q2+Q3*Q4 plotModel(qtl) # if formula given, the attribute within the object is ignored plotModel(qtl, y~Q1+Q2+Q3+Q4) # NULL formula indicates additive QTL model plotModel(qtl, NULL) # reorder the QTL in the figure plotModel(qtl, order=c(1,3,4,2)) # show just the chromosome numbers plotModel(qtl, chronly=TRUE) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>