info(LOGGER, "retaining motifs occurring at least %d times with a " +
"z-score at or above %f", minOccurrences, minZScore);
boolean isMultigraph = opts.hasOption('m');
boolean isDirected = opts.hasOption('d');
Fanmod fanmod = new Fanmod();
try {
if (isMultigraph && isDirected) {
DirectedMultigraph<String> dm =
GraphIO.readDirectedMultigraph(f, vertexLabels);
boolean findSimpleMotifs = opts.hasOption('s');
Map<Multigraph<String,DirectedTypedEdge<String>>,Fanmod.Result>
motifToZScore = fanmod.findMotifs(
dm, findSimpleMotifs, motifSize, numRandomGraphs, filter);
info(LOGGER, "found %d motifs with z-score above %f%n",
motifToZScore.size(), minZScore);
if (opts.hasOption('H')) {
File baseDir = new File(opts.getStringOption('H'));
// Check that we can create output in that directory
if (!baseDir.exists())
baseDir.mkdir();
DotIO dio = new DotIO();
// Generate a consistent set of edge colors to user across
// all the motif visualizations
Map<String,Color> edgeColors = new HashMap<String,Color>();
ColorGenerator cg = new ColorGenerator();
for (String type : dm.edgeTypes())
edgeColors.put(type, cg.next());
PrintWriter pw = new PrintWriter(new File(baseDir, "index.html"));
PrintWriter imgScript = new PrintWriter(new File(baseDir, "img-script.sh"));
imgScript.println("#!/bin/bash");
pw.println("<html>");
pw.println("<head><script src=\"http://www.kryogenix.org/code/browser/sorttable/sorttable.js\"></script></head>");
// pw.println("<head><script src=\"sorttable.js\"></script></head>");
pw.println("<body><table border=\"2\" class=\"sortable\">");
pw.println(" <tr>" +
"<td><h1><u>Motif</u></h1></td>" +
"<td><h1><u>Count</u></h1></td>" +
"<td><h1><u>Z-Score</u></h1></td>" +
"<td><h1><u>Mean Count in Random Graphs</u></h1></td>" +
"<td><h1><u>StdDev in Random Graphs</u></h1></td>" +
"</tr>");
int graphNum = 0;
for (Map.Entry<Multigraph<String,DirectedTypedEdge<String>>,Fanmod.Result> e :
motifToZScore.entrySet()) {
File dotFile = new File(baseDir, "graph-" + (graphNum++) + ".dot");
dio.writeDirectedMultigraph(e.getKey(), dotFile, edgeColors);
String imgFile = dotFile.getName();
imgFile = imgFile.substring(0, imgFile.length() - 3) + "gif";
imgScript.printf("dot -Tgif %s -o %s%n", dotFile.getName(), imgFile);
int count = e.getValue().count;
double zScore = e.getValue().statistic;
double mean = e.getValue().meanCountInNullModel;
double stddev = e.getValue().stddevInNullModel;
pw.printf(" <tr><td><img src=\"%s\"></td><td>%d</td><td>%f</td><td>%f</td><td>%f</td></tr>%n",
imgFile, count, zScore, mean, stddev);
}
pw.println("</table></body></html>");
imgScript.close();
pw.close();
}
info(LOGGER, "writing final motifs to %s",
opts.getPositionalArg(1));
// Write the results to file
File output = new File(opts.getPositionalArg(1));
// Copy the motifs to a new HashSet to avoid writing the result
// as a KeySet, which includes the fanmod result values.
SerializableUtil.save(
new HashSet<Multigraph<String,
DirectedTypedEdge<String>>>(motifToZScore.keySet()), output);
}
else if (isMultigraph) {
boolean findSimpleMotifs = opts.hasOption('s');
UndirectedMultigraph<String> um =
GraphIO.readUndirectedMultigraph(f, vertexLabels);
Map<Multigraph<String,TypedEdge<String>>,Fanmod.Result>
motifToZScore = fanmod.findMotifs(
um, findSimpleMotifs, motifSize, numRandomGraphs, filter);
info(LOGGER, "found %d motifs with z-score above %f%n",
motifToZScore.size(), minZScore);
if (opts.hasOption('H')) {
File baseDir = new File(opts.getStringOption('H'));