EVOLUTION-MANAGER
Edit File: plot.pxg.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 phenotypes versus marker genotypes</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 plotPXG {qtl}"><tr><td>plotPXG {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot phenotypes versus marker genotypes</h2> <h3>Description</h3> <p>Plot the phenotype values versus the genotypes at a marker or markers. </p> <h3>Usage</h3> <pre> plotPXG(x, marker, pheno.col=1, jitter=1, infer=TRUE, pch, ylab, main, col, ...) </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>marker</code></td> <td> <p>Marker name (a character string; can be a vector).</p> </td></tr> <tr valign="top"><td><code>pheno.col</code></td> <td> <p>Column number in the phenotype matrix which should be used as the phenotype. One may also give a character string matching a phenotype name. Finally, one may give a numeric vector of phenotypes, in which case it must have the length equal to the number of individuals in the cross, and there must be either non-integers or values < 1 or > no. phenotypes; this last case may be useful for studying transformations.</p> </td></tr> <tr valign="top"><td><code>jitter</code></td> <td> <p>A positive number indicating how much to spread out the points horizontally. (Larger numbers correspond to greater spread.)</p> </td></tr> <tr valign="top"><td><code>infer</code></td> <td> <p>If TRUE, missing genotypes are filled in with a single random imputation and plotted in red; if FALSE, only individuals typed at the specified marker are plotted.</p> </td></tr> <tr valign="top"><td><code>pch</code></td> <td> <p>Plot symbol.</p> </td></tr> <tr valign="top"><td><code>ylab</code></td> <td> <p>Label for y-axis.</p> </td></tr> <tr valign="top"><td><code>main</code></td> <td> <p>Main title for the plot. If missing, the names of the markers are used.</p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p>A vector of colors to use for the confidence intervals (optional).</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to <code><a href="../../graphics/html/plot.html">plot</a></code>.</p> </td></tr> </table> <h3>Details</h3> <p>Plots the phenotype data against the genotypes at the specified marker. If infer=TRUE, the genotypes of individuals that were not typed is inferred based the genotypes at linked markers via a single imputation from <code><a href="sim.geno.html">sim.geno</a></code>; these points are plotted in red. For each genotype, the phenotypic mean is plotted, with error bars at <i>+/-</i> 1 SE. </p> <h3>Value</h3> <p>A data.frame with initial columns the marker genotypes, then the phenotype data, then a column indicating whether any of the marker genotypes were inferred (1=at least one genotype inferred, 0=none were inferred). </p> <h3>Author(s)</h3> <p>Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a>; Brian Yandell </p> <h3>See Also</h3> <p><code><a href="find.marker.html">find.marker</a></code>, <code><a href="effectplot.html">effectplot</a></code>, <code><a href="find.flanking.html">find.flanking</a></code>, <code><a href="effectscan.html">effectscan</a></code> </p> <h3>Examples</h3> <pre> data(listeria) mname <- find.marker(listeria, 5, 28) # marker D5M357 plotPXG(listeria, mname) mname2 <- find.marker(listeria, 13, 26) # marker D13Mit147 plotPXG(listeria, c(mname, mname2)) plotPXG(listeria, c(mname2, mname)) # output of the function contains the raw data output <- plotPXG(listeria, mname) head(output) # another example data(fake.f2) mname <- find.marker(fake.f2, 1, 37) # marker D1M437 plotPXG(fake.f2, mname) mname2 <- find.marker(fake.f2, "X", 14) # marker DXM66 plotPXG(fake.f2, mname2) plotPXG(fake.f2, c(mname,mname2)) plotPXG(fake.f2, c(mname2,mname)) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>