Package edu.ucla.sspace.graph.io

Examples of edu.ucla.sspace.graph.io.DotIO


                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'));
                    // 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 : um.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,TypedEdge<String>>,Fanmod.Result> e :
                             motifToZScore.entrySet()) {
                        File dotFile = new File(baseDir, "graph-" + (graphNum++) + ".dot");
                        dio.writeUndirectedMultigraph(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;
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