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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: Plot LOD curves</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.scanone {qtl}"><tr><td>plot.scanone {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot LOD curves</h2> <h3>Description</h3> <p>Plot the LOD curve for a genome scan with a single-QTL model (the output of <code><a href="scanone.html">scanone</a></code>). </p> <h3>Usage</h3> <pre> ## S3 method for class 'scanone' plot(x, x2, x3, chr, lodcolumn=1, incl.markers=TRUE, xlim, ylim, lty=1, col=c("black","blue","red"), lwd=2, add=FALSE, gap=25, mtick = c("line", "triangle"), show.marker.names=FALSE, alternate.chrid=FALSE, bandcol=NULL, type="l", cex=1, pch=1, bg="transparent", bgrect=NULL, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>"scanone"</code>, as output by <code><a href="scanone.html">scanone</a></code>.</p> </td></tr> <tr valign="top"><td><code>x2</code></td> <td> <p>Optional second <code>scanone</code> object.</p> </td></tr> <tr valign="top"><td><code>x3</code></td> <td> <p>Optional third <code>scanone</code> object.</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>lodcolumn</code></td> <td> <p>An integer, or vector of 3 integers, indicating which of the LOD score columns should be plotted (generally this is 1).</p> </td></tr> <tr valign="top"><td><code>incl.markers</code></td> <td> <p>Indicate whether to plot line segments at the marker locations.</p> </td></tr> <tr valign="top"><td><code>xlim</code></td> <td> <p>Limits for x-axis (optional).</p> </td></tr> <tr valign="top"><td><code>ylim</code></td> <td> <p>Limits for y-axis (optional).</p> </td></tr> <tr valign="top"><td><code>lty</code></td> <td> <p>Line types; a vector of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p>Line colors; a vector of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>lwd</code></td> <td> <p>Line widths; a vector of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>add</code></td> <td> <p>If TRUE, add to a current plot.</p> </td></tr> <tr valign="top"><td><code>gap</code></td> <td> <p>Gap separating chromosomes (in cM).</p> </td></tr> <tr valign="top"><td><code>mtick</code></td> <td> <p>Tick mark type for markers (line segments or upward-pointing triangels).</p> </td></tr> <tr valign="top"><td><code>show.marker.names</code></td> <td> <p>If TRUE, show the marker names along the x axis.</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>bandcol</code></td> <td> <p>Optional color for alternating bands to indicate chromosomes. If NULL (the default), no bands are plotted. A good choice might be <code>bandcol="gray70"</code>.</p> </td></tr> <tr valign="top"><td><code>type</code></td> <td> <p>Type of plot (see <code><a href="../../graphics/html/plot.html">plot</a></code>): for example, <code>type="l"</code> for lines or <code>type="p"</code> for points only, may be of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>cex</code></td> <td> <p>Point size expansion, for example if <code>type="p"</code> is used. May be of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>pch</code></td> <td> <p>Point type, for example if <code>type="p"</code> is used. See <code><a href="../../graphics/html/points.html">points</a></code>. May be of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>bg</code></td> <td> <p>Background color for points, for example if <code>type="p"</code> and <code>pch=21</code> are used. See <code><a href="../../graphics/html/points.html">points</a></code>. May be of length 1 or 3.</p> </td></tr> <tr valign="top"><td><code>bgrect</code></td> <td> <p>Optional background color for the rectangular plotting region.</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> when it is called.</p> </td></tr> </table> <h3>Details</h3> <p>This function allows you to plot the results of up to three genome scans against one another. Such objects must conform with each other. </p> <p>One may alternatively use the argument <code>add</code> to add the plot of an additional genome scan to the current figure, but some care is required: the same chromosomes should be selected, and the results must concern crosses with the same genetic maps. </p> <p>If a single <code>scanone</code> object containing multiple LOD score columns (for example, from different phenotypes) is input, up to three LOD curves may be plotted, by providing a vector in the argument <code>lodcolumn</code>. If multiple <code>scanone</code> objects are input (via <code>x</code>, <code>x2</code> and <code>x3</code>), the LOD score columns to be plotted are chosen from the corresponding element of the <code>lodcolumn</code> argument. </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="scanone.html">scanone</a></code>, <code><a href="summary.scanone.html">summary.scanone</a></code>, <code><a href="../../graphics/html/par.html">par</a></code>, <code><a href="../../grDevices/html/colors.html">colors</a></code>, <code><a href="add.threshold.html">add.threshold</a></code>, <code><a href="xaxisloc.scanone.html">xaxisloc.scanone</a></code> </p> <h3>Examples</h3> <pre> data(fake.f2) fake.f2 <- calc.genoprob(fake.f2,step=2.5) out.mr <- scanone(fake.f2, method="mr") out.em <- scanone(fake.f2, method="em") plot(out.mr) plot(out.mr, out.em, chr=c(1,13), lty=1, col=c("violetred","black")) out.hk <- scanone(fake.f2, method="hk") plot(out.hk, chr=c(1,13), add=TRUE, col="slateblue") plot(out.hk, chr=13, show.marker.names=TRUE) plot(out.hk, bandcol="gray70") # plot points rather than lines plot(out.hk, bandcol="gray70", type="p", cex=0.3, pch=21, bg="slateblue") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>