EVOLUTION-MANAGER
Edit File: plot.errorlod.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 grid of error LOD values</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 plotErrorlod {qtl}"><tr><td>plotErrorlod {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot grid of error LOD values</h2> <h3>Description</h3> <p>Plot a grid of the LOD scores indicating which genotypes are likely to be in error. </p> <h3>Usage</h3> <pre> plotErrorlod(x, chr, ind, breaks=c(-Inf,2,3,4.5,Inf), col=c("white","gray85","hotpink","purple3"), alternate.chrid=FALSE, ...) </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 be drawn in the 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>ind</code></td> <td> <p>Indicates the individuals for which the error LOD scores should be plotted (passed to <code><a href="subset.cross.html">subset.cross</a></code>).</p> </td></tr> <tr valign="top"><td><code>breaks</code></td> <td> <p>A set of breakpoints for the colors; must give one more breakpoint than color. Intervals are open on the left and closed on the right, except for the lowest interval.</p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p>A vector of colors to appear in the image.</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>...</code></td> <td> <p>Ignored at this point.</p> </td></tr> </table> <h3>Details</h3> <p>Uses <code><a href="../../graphics/html/image.html">image</a></code> to plot a grid with different shades of pixels to indicate which genotypes are likely to be in error. </p> <p>Darker pixels have higher error LOD scores: <i>LOD ≤ 2</i> in white; <i>2 < LOD <= 3</i> in gray; <i>3 < LOD <= 4.5</i> in pink; <i>LOD > 4.5</i> in purple. </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>References</h3> <p>Lincoln, S. E. and Lander, E. S. (1992) Systematic detection of errors in genetic linkage data. <em>Genomics</em> <b>14</b>, 604–610. </p> <h3>See Also</h3> <p><code><a href="calc.errorlod.html">calc.errorlod</a></code>, <code><a href="top.errorlod.html">top.errorlod</a></code>, <code><a href="../../graphics/html/image.html">image</a></code>, <code><a href="subset.cross.html">subset.cross</a></code>, <code><a href="plot.geno.html">plotGeno</a></code> </p> <h3>Examples</h3> <pre> data(hyper) # Calculate error LOD scores hyper <- calc.errorlod(hyper,error.prob=0.01) # plot the error LOD scores; print those above a specified cutoff plotErrorlod(hyper) plotErrorlod(hyper,chr=1) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>