EVOLUTION-MANAGER
Edit File: plot.scanPhyloQTL.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 LOD curves from single-QTL scan to map QTL to a...</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.scanPhyloQTL {qtl}"><tr><td>plot.scanPhyloQTL {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot LOD curves from single-QTL scan to map QTL to a phylogenetic tree</h2> <h3>Description</h3> <p>Plot the LOD curves for each partition for a genome scan with a single diallelic QTL (the output of <code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>). </p> <h3>Usage</h3> <pre> ## S3 method for class 'scanPhyloQTL' plot(x, chr, incl.markers=TRUE, col, xlim, ylim, lwd=2, gap=25, mtick=c("line", "triangle"), show.marker.names=FALSE, alternate.chrid=FALSE, legend=TRUE, ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An object of class <code>"scanPhyloQTL"</code>, as output by <code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>.</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>incl.markers</code></td> <td> <p>Indicate whether to plot line segments at the marker locations.</p> </td></tr> <tr valign="top"><td><code>col</code></td> <td> <p>Optional vector of colors to use for each partition.</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>lwd</code></td> <td> <p>Line width.</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>legend</code></td> <td> <p>Indicates whether to include a legend in the plot.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to the function <code><a href="plot.scanone.html">plot.scanone</a></code> when it is called.</p> </td></tr> </table> <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>Broman, K. W., Kim, S., An\'e, C. and Payseur, B. A. Mapping quantitative trait loci to a phylogenetic tree. In preparation. </p> <h3>See Also</h3> <p><code><a href="scanPhyloQTL.html">scanPhyloQTL</a></code>, <code><a href="max.scanPhyloQTL.html">max.scanPhyloQTL</a></code>, <code><a href="summary.scanPhyloQTL.html">summary.scanPhyloQTL</a></code>, <code><a href="plot.scanone.html">plot.scanone</a></code>, <code><a href="inferredpartitions.html">inferredpartitions</a></code>, <code><a href="simPhyloQTL.html">simPhyloQTL</a></code>, <code><a href="../../graphics/html/par.html">par</a></code>, <code><a href="../../grDevices/html/colors.html">colors</a></code> </p> <h3>Examples</h3> <pre> ## Not run: # example map; drop X chromosome data(map10) map10 <- map10[1:19] # simulate data x <- simPhyloQTL(4, partition="AB|CD", crosses=c("AB", "AC", "AD"), map=map10, n.ind=150, model=c(1, 50, 0.5, 0)) # run calc.genoprob on each cross x <- lapply(x, calc.genoprob, step=2) # scan genome, at each position trying all possible partitions out <- scanPhyloQTL(x, method="hk") # maximum peak max(out, format="lod") # approximate posterior probabilities at peak max(out, format="postprob") # all peaks above a threshold for LOD(best) - LOD(2nd best) summary(out, threshold=1, format="lod") # all peaks above a threshold for LOD(best), showing approx post'r prob summary(out, format="postprob", threshold=3) # plot of results plot(out) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>