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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 scores for a two-dimensional genome scan</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.scantwo {qtl}"><tr><td>plot.scantwo {qtl}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>Plot LOD scores for a two-dimensional genome scan</h2> <h3>Description</h3> <p>Plot the results of a two-dimensional, two-QTL genome scan. </p> <h3>Usage</h3> <pre> ## S3 method for class 'scantwo' plot(x, chr, incl.markers=FALSE, zlim, lodcolumn=1, lower = c("full", "add", "cond-int", "cond-add", "int"), upper = c("int", "cond-add", "cond-int", "add", "full"), nodiag=TRUE, contours=FALSE, main, zscale=TRUE, point.at.max=FALSE, col.scheme = c("viridis", "redblue","cm","gray","heat","terrain","topo"), gamma=0.6, allow.neg=FALSE, 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>"scantwo"</code>, as output by <code><a href="scantwo.html">scantwo</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>If FALSE, plot LOD scores on an evenly spaced grid (not including the results at the markers).</p> </td></tr> <tr valign="top"><td><code>zlim</code></td> <td> <p>A vector of length 2 (optional), indicating the z limits for the lower-right and upper-left triangles, respectively. If one number is given, the same limits are used for both triangles. If <code>zlim</code> is missing, the maximum limits are used for each.</p> </td></tr> <tr valign="top"><td><code>lodcolumn</code></td> <td> <p>If the scantwo results contain LOD scores for multiple phenotypes, this argument indicates which to use in the plot.</p> </td></tr> <tr valign="top"><td><code>lower</code></td> <td> <p>Indicates which LOD scores should be plotted in the lower triangle. See the details below.</p> </td></tr> <tr valign="top"><td><code>upper</code></td> <td> <p>Indicates which LOD scores should be plotted in the upper triangle. See the details below.</p> </td></tr> <tr valign="top"><td><code>nodiag</code></td> <td> <p>If TRUE, suppress the plot of the scanone output (which is normally along the diagonal.)</p> </td></tr> <tr valign="top"><td><code>contours</code></td> <td> <p>If TRUE, add a contour to the plot at 1.5-LOD below its maximum, using a call to <code><a href="../../graphics/html/contour.html">contour</a></code>. If a numeric vector, contours are drawn at these values below the maximum LOD.</p> </td></tr> <tr valign="top"><td><code>main</code></td> <td> <p>An optional title for the plot.</p> </td></tr> <tr valign="top"><td><code>zscale</code></td> <td> <p>If TRUE, a color scale is plotted at the right.</p> </td></tr> <tr valign="top"><td><code>point.at.max</code></td> <td> <p>If TRUE, plot an X at the maximum LOD.</p> </td></tr> <tr valign="top"><td><code>col.scheme</code></td> <td> <p>Name of color pallet. 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>gamma</code></td> <td> <p>Parameter affecting range of colors when <code>col.scheme="gray"</code> or <code>="redblue"</code>.</p> </td></tr> <tr valign="top"><td><code>allow.neg</code></td> <td> <p>If TRUE, allow the plot of negative LOD scores; in this case, the z-limits are symmetric about 0. This option is chiefly to allow a plot of difference between LOD scores from different methods, calculated via <code><a href="arithscan.html">-.scantwo</a></code>.</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 of LOD scores. The particular LOD scores plotted in the upper-left and lower-right triangles are selected via <code>upper</code> and <code>lower</code>, respectively. By default, the upper-left triangle contains the epistasis LOD scores (<code>"int"</code>), and the lower-right triangle contains the LOD scores for the full model (<code>"full"</code>). The diagonal contains either all zeros or the main effects LOD scores (from <code><a href="scanone.html">scanone</a></code>). </p> <p>The <code><a href="scantwo.html">scantwo</a></code> function calculates, for each pair of putative QTLs, <i>(q1,q2)</i>, the likelihood under the null model <i>L0</i>, the likelihood under each of the single-QTL models, <i>L(q1)</i> and <i>L(q2)</i>, the likelihood under an additive QTL model, <i>La(q1,q2)</i>, and the likelihood under a full QTL model (including QTL-QTL interaction), <i>Lf(q1,q2)</i>. </p> <p>The five possible LOD scores that may be plotted are the following. The epistasis LOD scores (<code>"int"</code>) are <i>LODi = log10 Lf(q1,q2) - log10 La(q1,q2)</i>. </p> <p>The full LOD scores (<code>"full"</code>) are <i> LODj = log10 Lf(q1,q2) - log10 L0</i>. </p> <p>The additive LOD scores (<code>"add"</code>) are <i> LODa = log10 La(q1,q2) - log10 L0</i>. </p> <p>In addition, we may calculate, for each pair of chromosomes, the difference between the full LOD score and the maximum single-QTL LOD scores for that pair of chromosomes (<code>"cond-int"</code>). </p> <p>Finally, we may calculate, for each pair of chromosomes, the difference between the additive LOD score and the maximum single-QTL LOD scores for that pair of chromosomes (<code>"cond-add"</code>). </p> <p>If a color scale is plotted (<code>zscale=TRUE</code>), the axis on the left indicates the scale for the upper-left triangle, while the axis on the right indicates the scale for the lower-right triangle. Note that the axis labels can get screwed up if you change the size of the figure window; you'll need to redo the plot. </p> <h3>Value</h3> <p>None.</p> <h3>Output of addpair</h3> <p><b>Note</b> that, for output from <code><a href="addpair.html">addpair</a></code> in which the new loci are indicated explicitly in the formula, the summary provided by <code>plot.scantwo</code> is somewhat special. In particular, the <code>lower</code> and <code>upper</code> arguments are ignored. </p> <p>In the case that the formula used in <code><a href="addpair.html">addpair</a></code> was not symmetric in the two new QTL, the x-axis in the plot corresponds to the first of the new QTL and the y-axis corresponds to the second of the new QTL. </p> <h3>Author(s)</h3> <p>Hao Wu; Karl W Broman, <a href="mailto:broman@wisc.edu">broman@wisc.edu</a>; Brian Yandell </p> <h3>See Also</h3> <p><code><a href="scantwo.html">scantwo</a></code>, <code><a href="summary.scantwo.html">summary.scantwo</a></code>, <code><a href="plot.scanone.html">plot.scanone</a></code>, <code><a href="arithscan.html">-.scantwo</a></code> </p> <h3>Examples</h3> <pre> data(hyper) hyper <- calc.genoprob(hyper, step=5) # 2-d scan by EM and by Haley-Knott regression out2.em <- scantwo(hyper, method="em") out2.hk <- scantwo(hyper, method="hk") # plot epistasis and full LOD scores plot(out2.em) # plot cond-int in upper triangle and full in lower triangle # for chromosomes 1, 4, 6, 15 plot(out2.em, upper="cond-int", chr=c(1,4,6,15)) # plot cond-add in upper triangle and add in lower triangle # for chromosomes 1, 4 plot(out2.em, upper="cond-add", lower="add", chr=c(1,4)) # plot the differences between the LOD scores from Haley-Knott # regression and the EM algorithm plot(out2.hk - out2.em, allow.neg=TRUE) </pre> <hr /><div style="text-align: center;">[Package <em>qtl</em> version 1.46-2 <a href="00Index.html">Index</a>]</div> </body></html>