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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 recombination fractions</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 plotRF {qtl}"><tr><td>plotRF {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot recombination fractions</h2> <h3>Description</h3> <p>Plot a grid showing the recombination fractions for all pairs of markers, and/or the LOD scores for tests of linkage between pairs of markers. </p> <h3>Usage</h3> <pre> plotRF(x, chr, what=c("both","lod","rf"), alternate.chrid=FALSE, zmax=12, mark.diagonal=FALSE, col.scheme=c("viridis", "redblue"), ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>cross</code>. See <code><a href="read.cross.html">read.cross</a></code> for details.</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>what</code></td> <td> <p>Indicate whether to plot LOD scores, recombination fractions or both.</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>zmax</code></td> <td> <p>Maximum LOD score plotted; values above this are all thresholded at this value.</p> </td></tr> <tr valign="top"><td><code>mark.diagonal</code></td> <td> <p>If TRUE, include black line segments around the pixels along the diagonal, to better separate the upper left triangle from the lower right triangle.</p> </td></tr> <tr valign="top"><td><code>col.scheme</code></td> <td> <p>The color palette. The default is "viridis"; see Option D at <a href="https://bids.github.io/colormap">https://bids.github.io/colormap</a></p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Generally ignored, but you can include <code>main</code> to change or omit the title of the figure.</p> </td></tr> </table> <h3>Details</h3> <p>Uses <code><a href="../../graphics/html/image.html">image</a></code> to plot a grid showing the recombination fractions and/or LOD scores for all pairs of markers. (The LOD scores are for a test of <i>r = 1/2</i>.) If both are plotted, the recombination fractions are in the upper left triangle while the LOD scores are in the lower right triangle. </p> <p>With <code>col.scheme="viridis"</code> (the default), purple corresponds to a large LOD score or a small recombination fraction, while yellow is the reverse. With <code>col.scheme="redblue"</code>, red corresponds to a large LOD or a small recombination fraction, while blue is the reverse. Note that missing values appear in light gray. </p> <p>Recombination fractions are transformed by <i> -4(log2(r)+1)</i> to make them on the same sort of scale as LOD scores. Values of LOD or the transformed recombination fraction that are above 12 are set to 12. </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="est.rf.html">est.rf</a></code>, <code><a href="pull.rf.html">pull.rf</a></code>, <code><a href="plot.rfmatrix.html">plot.rfmatrix</a></code>, <code><a href="../../graphics/html/image.html">image</a></code>, <code><a href="badorder.html">badorder</a></code>, <code><a href="ripple.html">ripple</a></code> </p> <h3>Examples</h3> <pre> data(badorder) badorder <- est.rf(badorder) plotRF(badorder) # plot just chr 1 plotRF(badorder, chr=1) # plot just the recombination fractions plotRF(badorder, what="rf") # plot just the LOD scores, and just for chr 2 and 3 plotRF(badorder, chr=2:3, what="lod") </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>