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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: HRG dendrogram plot</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_dendrogram.igraphHRG {igraph}"><tr><td>plot_dendrogram.igraphHRG {igraph}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>HRG dendrogram plot</h2> <h3>Description</h3> <p>Plot a hierarchical random graph as a dendrogram. </p> <h3>Usage</h3> <pre> ## S3 method for class 'igraphHRG' plot_dendrogram(x, mode = igraph_opt("dend.plot.type"), ...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>x</code></td> <td> <p>An <code>igraphHRG</code>, a hierarchical random graph, as returned by the <code><a href="fit_hrg.html">fit_hrg</a></code> function.</p> </td></tr> <tr valign="top"><td><code>mode</code></td> <td> <p>Which dendrogram plotting function to use. See details below.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Additional arguments to supply to the dendrogram plotting function.</p> </td></tr> </table> <h3>Details</h3> <p><code>plot_dendrogram</code> supports three different plotting functions, selected via the <code>mode</code> argument. By default the plotting function is taken from the <code>dend.plot.type</code> igraph option, and it has for possible values: </p> <ul> <li> <p><code>auto</code> Choose automatically between the plotting functions. As <code>plot.phylo</code> is the most sophisticated, that is choosen, whenever the <code>ape</code> package is available. Otherwise <code>plot.hclust</code> is used. </p> </li> <li> <p><code>phylo</code> Use <code>plot.phylo</code> from the <code>ape</code> package. </p> </li> <li> <p><code>hclust</code> Use <code>plot.hclust</code> from the <code>stats</code> package. </p> </li> <li> <p><code>dendrogram</code> Use <code>plot.dendrogram</code> from the <code>stats</code> package. </p> </li></ul> <p>The different plotting functions take different sets of arguments. When using <code>plot.phylo</code> (<code>mode="phylo"</code>), we have the following syntax: </p> <pre> plot_dendrogram(x, mode="phylo", colbar = rainbow(11, start=0.7, end=0.1), edge.color = NULL, use.edge.length = FALSE, \dots) </pre><p> The extra arguments not documented above: </p> <ul> <li> <p><code>colbar</code> Color bar for the edges. </p> </li> <li> <p><code>edge.color</code> Edge colors. If <code>NULL</code>, then the <code>colbar</code> argument is used. </p> </li> <li> <p><code>use.edge.length</code> Passed to <code>plot.phylo</code>. </p> </li> <li> <p><code>dots</code> Attitional arguments to pass to <code>plot.phylo</code>. </p> </li></ul> <p>The syntax for <code>plot.hclust</code> (<code>mode="hclust"</code>): </p> <pre> plot_dendrogram(x, mode="hclust", rect = 0, colbar = rainbow(rect), hang = 0.01, ann = FALSE, main = "", sub = "", xlab = "", ylab = "", \dots) </pre><p> The extra arguments not documented above: </p> <ul> <li> <p><code>rect</code> A numeric scalar, the number of groups to mark on the dendrogram. The dendrogram is cut into exactly <code>rect</code> groups and they are marked via the <code>rect.hclust</code> command. Set this to zero if you don't want to mark any groups. </p> </li> <li> <p><code>colbar</code> The colors of the rectangles that mark the vertex groups via the <code>rect</code> argument. </p> </li> <li> <p><code>hang</code> Where to put the leaf nodes, this corresponds to the <code>hang</code> argument of <code>plot.hclust</code>. </p> </li> <li> <p><code>ann</code> Whether to annotate the plot, the <code>ann</code> argument of <code>plot.hclust</code>. </p> </li> <li> <p><code>main</code> The main title of the plot, the <code>main</code> argument of <code>plot.hclust</code>. </p> </li> <li> <p><code>sub</code> The sub-title of the plot, the <code>sub</code> argument of <code>plot.hclust</code>. </p> </li> <li> <p><code>xlab</code> The label on the horizontal axis, passed to <code>plot.hclust</code>. </p> </li> <li> <p><code>ylab</code> The label on the vertical axis, passed to <code>plot.hclust</code>. </p> </li> <li> <p><code>dots</code> Attitional arguments to pass to <code>plot.hclust</code>. </p> </li></ul> <p>The syntax for <code>plot.dendrogram</code> (<code>mode="dendrogram"</code>): </p> <pre> plot_dendrogram(x, \dots) </pre><p> The extra arguments are simply passed to <code>as.dendrogram</code>. </p> <h3>Value</h3> <p>Returns whatever the return value was from the plotting function, <code>plot.phylo</code>, <code>plot.dendrogram</code> or <code>plot.hclust</code>. </p> <h3>Author(s)</h3> <p>Gabor Csardi <a href="mailto:csardi.gabor@gmail.com">csardi.gabor@gmail.com</a> </p> <h3>Examples</h3> <pre> g <- make_full_graph(5) + make_full_graph(5) hrg <- fit_hrg(g) plot_dendrogram(hrg) </pre> <hr /><div style="text-align: center;">[Package <em>igraph</em> version 1.3.5 <a href="00Index.html">Index</a>]</div> </body></html>