EVOLUTION-MANAGER
Edit File: layout_with_drl.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: The DrL graph layout generator</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 layout_with_drl {igraph}"><tr><td>layout_with_drl {igraph}</td><td style="text-align: right;">R Documentation</td></tr></table> <h2>The DrL graph layout generator</h2> <h3>Description</h3> <p>DrL is a force-directed graph layout toolbox focused on real-world large-scale graphs, developed by Shawn Martin and colleagues at Sandia National Laboratories. </p> <h3>Usage</h3> <pre> layout_with_drl( graph, use.seed = FALSE, seed = matrix(runif(vcount(graph) * 2), ncol = 2), options = drl_defaults$default, weights = NULL, fixed = NULL, dim = 2 ) with_drl(...) </pre> <h3>Arguments</h3> <table summary="R argblock"> <tr valign="top"><td><code>graph</code></td> <td> <p>The input graph, in can be directed or undirected.</p> </td></tr> <tr valign="top"><td><code>use.seed</code></td> <td> <p>Logical scalar, whether to use the coordinates given in the <code>seed</code> argument as a starting point.</p> </td></tr> <tr valign="top"><td><code>seed</code></td> <td> <p>A matrix with two columns, the starting coordinates for the vertices is <code>use.seed</code> is <code>TRUE</code>. It is ignored otherwise.</p> </td></tr> <tr valign="top"><td><code>options</code></td> <td> <p>Options for the layout generator, a named list. See details below.</p> </td></tr> <tr valign="top"><td><code>weights</code></td> <td> <p>The weights of the edges. It must be a positive numeric vector, <code>NULL</code> or <code>NA</code>. If it is <code>NULL</code> and the input graph has a ‘weight’ edge attribute, then that attribute will be used. If <code>NULL</code> and no such attribute is present, then the edges will have equal weights. Set this to <code>NA</code> if the graph was a ‘weight’ edge attribute, but you don't want to use it for the layout. Larger edge weights correspond to stronger connections.</p> </td></tr> <tr valign="top"><td><code>fixed</code></td> <td> <p>Logical vector, it can be used to fix some vertices. Unfortunately this has never been implemented in the C core of the igraph library and thus it never worked. The argument is now deprecated and will be removed in igraph 1.4.0.</p> </td></tr> <tr valign="top"><td><code>dim</code></td> <td> <p>Either ‘2’ or ‘3’, it specifies whether we want a two dimensional or a three dimensional layout. Note that because of the nature of the DrL algorithm, the three dimensional layout takes significantly longer to compute.</p> </td></tr> <tr valign="top"><td><code>...</code></td> <td> <p>Passed to <code>layout_with_drl</code>.</p> </td></tr> </table> <h3>Details</h3> <p>This function implements the force-directed DrL layout generator. </p> <p>The generator has the following parameters: </p> <dl> <dt>edge.cut</dt><dd><p>Edge cutting is done in the late stages of the algorithm in order to achieve less dense layouts. Edges are cut if there is a lot of stress on them (a large value in the objective function sum). The edge cutting parameter is a value between 0 and 1 with 0 representing no edge cutting and 1 representing maximal edge cutting. </p> </dd> <dt>init.iterations</dt><dd><p>Number of iterations in the first phase.</p> </dd> <dt>init.temperature</dt><dd><p>Start temperature, first phase.</p> </dd> <dt>init.attraction</dt><dd><p>Attraction, first phase.</p> </dd> <dt>init.damping.mult</dt><dd><p>Damping, first phase.</p> </dd> <dt>liquid.iterations</dt><dd><p>Number of iterations, liquid phase.</p> </dd> <dt>liquid.temperature</dt><dd><p>Start temperature, liquid phase.</p> </dd> <dt>liquid.attraction</dt><dd><p>Attraction, liquid phase.</p> </dd> <dt>liquid.damping.mult</dt><dd><p>Damping, liquid phase.</p> </dd> <dt>expansion.iterations</dt><dd><p>Number of iterations, expansion phase.</p> </dd> <dt>expansion.temperature</dt><dd><p>Start temperature, expansion phase.</p> </dd> <dt>expansion.attraction</dt><dd><p>Attraction, expansion phase.</p> </dd> <dt>expansion.damping.mult</dt><dd><p>Damping, expansion phase.</p> </dd> <dt>cooldown.iterations</dt><dd><p>Number of iterations, cooldown phase.</p> </dd> <dt>cooldown.temperature</dt><dd><p>Start temperature, cooldown phase.</p> </dd> <dt>cooldown.attraction</dt><dd><p>Attraction, cooldown phase.</p> </dd> <dt>cooldown.damping.mult</dt><dd><p>Damping, cooldown phase.</p> </dd> <dt>crunch.iterations</dt><dd><p>Number of iterations, crunch phase.</p> </dd> <dt>crunch.temperature</dt><dd><p>Start temperature, crunch phase.</p> </dd> <dt>crunch.attraction</dt><dd><p>Attraction, crunch phase.</p> </dd> <dt>crunch.damping.mult</dt><dd><p>Damping, crunch phase.</p> </dd> <dt>simmer.iterations</dt><dd><p>Number of iterations, simmer phase.</p> </dd> <dt>simmer.temperature</dt><dd><p>Start temperature, simmer phase.</p> </dd> <dt>simmer.attraction</dt><dd><p>Attraction, simmer phase.</p> </dd> <dt>simmer.damping.mult</dt><dd><p>Damping, simmer phase.</p> </dd> </dl> <p>There are five pre-defined parameter settings as well, these are called <code>drl_defaults$default</code>, <code>drl_defaults$coarsen</code>, <code>drl_defaults$coarsest</code>, <code>drl_defaults$refine</code> and <code>drl_defaults$final</code>. </p> <h3>Value</h3> <p>A numeric matrix with two columns. </p> <h3>Author(s)</h3> <p>Shawn Martin (<a href="http://www.cs.otago.ac.nz/homepages/smartin/">http://www.cs.otago.ac.nz/homepages/smartin/</a>) and Gabor Csardi <a href="mailto:csardi.gabor@gmail.com">csardi.gabor@gmail.com</a> for the R/igraph interface and the three dimensional version. </p> <h3>References</h3> <p>See the following technical report: Martin, S., Brown, W.M., Klavans, R., Boyack, K.W., DrL: Distributed Recursive (Graph) Layout. SAND Reports, 2008. 2936: p. 1-10. </p> <h3>See Also</h3> <p><code><a href="layout_.html">layout</a></code> for other layout generators. </p> <h3>Examples</h3> <pre> g <- as.undirected(sample_pa(100, m=1)) l <- layout_with_drl(g, options=list(simmer.attraction=0)) ## Not run: plot(g, layout=l, vertex.size=3, vertex.label=NA) ## End(Not run) </pre> <hr /><div style="text-align: center;">[Package <em>igraph</em> version 1.3.5 <a href="00Index.html">Index</a>]</div> </body></html>