EVOLUTION-MANAGER
Edit File: plot.qtl.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 QTL locations</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 plot.qtl {qtl}"><tr><td>plot.qtl {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot QTL locations</h2> <h3>Description</h3> <p>Plot the locations of the QTL against a genetic map </p> <h3>Usage</h3> <pre> ## S3 method for class 'qtl' plot(x, chr, horizontal=FALSE, shift=TRUE, show.marker.names=FALSE, alternate.chrid=FALSE, justdots=FALSE, col="red", ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>"qtl"</code>, as produced by <code><a href="makeqtl.html">makeqtl</a></code>.</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>horizontal</code></td> <td> <p>Specifies whether the chromosomes should be plotted horizontally.</p> </td></tr> <tr valign="top"><td><code>shift</code></td> <td> <p>If TRUE, shift the first marker on each chromosome to be at 0 cM.</p> </td></tr> <tr valign="top"><td><code>show.marker.names</code></td> <td> <p>If TRUE, marker names are included.</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>justdots</code></td> <td> <p>If FALSE, just plot dots at the QTL, rather than arrows and QTL names.</p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p>Color used to plot indications of QTL</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to <code><a href="plot.map.html">plotMap</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>Creates a plot, via <code><a href="plot.map.html">plotMap</a></code>, and indicates the locations of the QTL in the input QTL object, <code>x</code>. </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.map.html">plotMap</a></code>, <code><a href="makeqtl.html">makeqtl</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) # take out several QTLs and make QTL object qc <- c("1", "6", "13") qp <- c(25.8, 33.6, 18.63) fake.f2 <- subset(fake.f2, chr=qc) fake.f2 <- calc.genoprob(fake.f2, step=2, err=0.001) qtl <- makeqtl(fake.f2, qc, qp, what="prob") plot(qtl) plot(qtl, justdots=TRUE, col="seagreen") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>