EVOLUTION-MANAGER
Edit File: xaxisloc.scanone.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: Get x-axis locations in scanone plot</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 xaxisloc.scanone {qtl}"><tr><td>xaxisloc.scanone {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Get x-axis locations in scanone plot</h2> <h3>Description</h3> <p>Get x-axis locations for given cM positions on given chromosomes in a plot from <code><a href="plot.scanone.html">plot.scanone</a></code>) </p> <h3>Usage</h3> <pre> xaxisloc.scanone(out, thechr, thepos, chr, gap=25) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>out</code></td> <td> <p>An object of class <code>"scanone"</code>, as output by <code><a href="scanone.html">scanone</a></code>. This must be identical to what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>thechr</code></td> <td> <p>Chromosome IDs at which x-axis locations are to be determined.</p> </td></tr> <tr valign="top"><td><code>thepos</code></td> <td> <p>Chromosome positions at which x-axis locations are to be determined.</p> </td></tr> <tr valign="top"><td><code>chr</code></td> <td> <p>Optional vector specifying which chromosomes were plotted. This must be identical to what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>gap</code></td> <td> <p>Gap separating chromosomes (in cM). This must be identical to what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>This function allows you to identify the x-axis locations in a plot of genome scan results, produced by <code><a href="plot.scanone.html">plot.scanone</a></code>. This is useful for adding annotations, such as text or arrows. </p> <p>The arguments <code>out</code>, <code>chr</code>, and <code>gap</code> must match what was used in the call to <code><a href="plot.scanone.html">plot.scanone</a></code>. </p> <p>The arguments <code>thechr</code> and <code>thepos</code> indicate the genomic positions for which x-axis locations are desired. If they both have length > 1, they must have the same length. If one has length > 1 and one has length 1, the one with length 1 is expanded to match. </p> <h3>Value</h3> <p>A numeric vector of x-axis locations.</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.scanone.html">plot.scanone</a></code>, <code><a href="add.threshold.html">add.threshold</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.genoprob(hyper) out <- scanone(hyper, method="hk") plot(out, chr=c(1, 4, 6, 15)) # add arrow and text to indicate peak LOD score mxout <- max(out) x <- xaxisloc.scanone(out, mxout$chr, mxout$pos, chr=c(1,4,6,15)) arrows(x+30, mxout$lod, x+5, mxout$lod, len=0.1, col="blue") text(x+35, mxout$lod, "the peak", col="blue", adj=c(0, 0.5)) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.66 <a href="00Index.html">Index</a>]</div> </body></html>