Examples with CyNetwork org.cytoscape.model.CyNetwork used on opensource projects

Example 6 with CyNetwork

use of org.cytoscape.model.CyNetwork in project EnrichmentMapApp by BaderLab.

the class LegacySessionLoadTest method test_1_LoadedLegacyData.

@Test
@SessionFile("em_session_2.2.cys")
public void test_1_LoadedLegacyData() throws Exception {
    EnrichmentMap map = getEnrichmentMap();
    assertEquals("EM1_Enrichment Map", map.getName());
    CyNetwork network = networkManager.getNetwork(map.getNetworkID());
    assertNotNull(network);
    assertEquals(1, map.getDataSetCount());
    assertEquals(14067, map.getNumberOfGenes());
    assertEquals(14067, map.getAllGenes().size());
    // Number of edges: 3339 - that's how many geneset similarity objects there should be!!!
    CyTable edgeTable = network.getDefaultEdgeTable();
    assertEquals(3339, edgeTable.getRowCount());
    EMCreationParameters params = map.getParams();
    String prefix = params.getAttributePrefix();
    assertEquals("EM1_", prefix);
    assertEquals(0.5, params.getCombinedConstant(), 0.0);
    assertFalse(params.isEMgmt());
    assertEquals("Geneset_Overlap", params.getEnrichmentEdgeType());
    assertTrue(params.isFDR());
    assertEquals(GreatFilter.HYPER, params.getGreatFilter());
    assertEquals(0.005, params.getPvalue(), 0.0);
    assertEquals(1.0, params.getPvalueMin(), 0.0);
    assertEquals(0.1, params.getQvalue(), 0.0);
    assertEquals(1.0, params.getQvalueMin(), 0.0);
    assertEquals(0.5, params.getSimilarityCutoff(), 0.0);
    assertEquals(SimilarityMetric.OVERLAP, params.getSimilarityMetric());
    //		assertFalse(params.isDistinctExpressionSets());
    String geneset1 = "RESOLUTION OF SISTER CHROMATID COHESION%REACTOME%REACT_150425.2";
    String geneset2 = "CHROMOSOME, CENTROMERIC REGION%GO%GO:0000775";
    Collection<CyRow> rows = edgeTable.getMatchingRows(CyNetwork.NAME, geneset1 + " (Geneset_Overlap) " + geneset2);
    assertEquals(1, rows.size());
    CyRow row = rows.iterator().next();
    assertEquals("Geneset_Overlap", row.get(CyEdge.INTERACTION, String.class));
    assertEquals(0.6097560975609756, EMStyleBuilder.Columns.EDGE_SIMILARITY_COEFF.get(row, prefix), 0.0);
    EMDataSet dataset = map.getDataSet("Dataset 1");
    assertNotNull(dataset);
    assertSame(map, dataset.getMap());
    assertEquals(Method.GSEA, dataset.getMethod());
    assertEquals(12653, dataset.getDataSetGenes().size());
    assertEquals(389, dataset.getGeneSetsOfInterest().getGeneSets().size());
    //		assertEquals(17259, dataset.getSetofgenesets().getGenesets().size()); // MKTODO why? what is this used for
    assertEndsWith(dataset.getSetOfGeneSets().getFilename(), "Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt");
    for (long suid : dataset.getNodeSuids()) {
        assertNotNull(network.getNode(suid));
    }
    GeneSet geneset = dataset.getGeneSetsOfInterest().getGeneSets().get("NCRNA PROCESSING%GO%GO:0034470");
    assertEquals(88, geneset.getGenes().size());
    assertEquals("NCRNA PROCESSING%GO%GO:0034470", geneset.getName());
    assertEquals("ncRNA processing", geneset.getDescription());
    assertEquals(Optional.of("GO"), geneset.getSource());
    SetOfEnrichmentResults enrichments = dataset.getEnrichments();
    assertEquals(4756, enrichments.getEnrichments().size());
    assertEndsWith(enrichments.getFilename1(), "gsea_report_for_ES12_1473194913081.xls");
    assertEndsWith(enrichments.getFilename2(), "gsea_report_for_NT12_1473194913081.xls");
    assertEquals("ES12", enrichments.getPhenotype1());
    assertEquals("NT12", enrichments.getPhenotype2());
    EnrichmentResult result = enrichments.getEnrichments().get("RIBONUCLEOSIDE TRIPHOSPHATE BIOSYNTHETIC PROCESS%GO%GO:0009201");
    assertTrue(result instanceof GSEAResult);
    GSEAResult gseaResult = (GSEAResult) result;
    assertEquals("RIBONUCLEOSIDE TRIPHOSPHATE BIOSYNTHETIC PROCESS%GO%GO:0009201", gseaResult.getName());
    assertEquals(0.42844063, gseaResult.getES(), 0.0);
    assertEquals(0.45225498, gseaResult.getFdrqvalue(), 0.0);
    assertEquals(1.0, gseaResult.getFwerqvalue(), 0.0);
    assertEquals(23, gseaResult.getGsSize());
    assertEquals(1.1938541, gseaResult.getNES(), 0.0);
    assertEquals(0.2457786, gseaResult.getPvalue(), 0.0);
    assertEquals(4689, gseaResult.getRankAtMax());
    assertEquals(Optional.of("GO"), gseaResult.getSource());
    GeneExpressionMatrix expressions = dataset.getExpressionSets();
    assertEquals(20326, expressions.getExpressionUniverse());
    assertEquals(3.686190609, expressions.getClosesttoZero(), 0.0);
    //		assertEndsWith(expressions.getFilename(), "MCF7_ExprMx_v2_names.gct");
    assertEquals(15380.42388, expressions.getMaxExpression(), 0.0);
    assertEquals(3.686190609, expressions.getMinExpression(), 0.0);
    assertEquals(20, expressions.getNumConditions());
    assertEquals(12653, expressions.getExpressionMatrix().size());
    assertEquals(12653, expressions.getExpressionMatrix_rowNormalized().size());
    GeneExpression expression = expressions.getExpressionMatrix().get(0);
    assertEquals("MOCOS", expression.getName());
    assertEquals("MOCOS (molybdenum cofactor sulfurase)", expression.getDescription());
    assertEquals(18, expression.getExpression().length);
    Ranking ranking = expressions.getRanks().get("GSEARanking");
    assertEquals(12653, ranking.getAllRanks().size());
    assertEquals(12653, ranking.getRanking().size());
    Rank rank = ranking.getRanking().get(0);
    assertEquals("MOCOS", rank.getName());
    assertEquals(1238, rank.getRank().intValue());
    assertEquals(0.54488367, rank.getScore(), 0.0);
    DataSetFiles files = dataset.getDataSetFiles();
    assertEndsWith(files.getClassFile(), "ES_NT.cls");
    assertEndsWith(files.getEnrichmentFileName1(), "gsea_report_for_ES12_1473194913081.xls");
    assertEndsWith(files.getEnrichmentFileName2(), "gsea_report_for_NT12_1473194913081.xls");
    //		assertEndsWith(files.getExpressionFileName(), "MCF7_ExprMx_v2_names.gct");
    assertEndsWith(files.getGMTFileName(), "Human_GO_AllPathways_no_GO_iea_April_15_2013_symbol.gmt");
    assertEndsWith(files.getGseaHtmlReportFile(), "estrogen_treatment_12hr_gsea_enrichment_results.Gsea.1473194913081/index.html");
    assertEndsWith(files.getRankedFile(), "ranked_gene_list_ES12_versus_NT12_1473194913081.xls");
    assertEquals("ES12", files.getPhenotype1());
    assertEquals("NT12", files.getPhenotype2());
}

Example 7 with CyNetwork

use of org.cytoscape.model.CyNetwork in project EnrichmentMapApp by BaderLab.

the class CreateEnrichmentMapTaskTest method testEnrichmentMapBuildMapTask.

@Test
public void testEnrichmentMapBuildMapTask() throws Exception {
    String geneSetsFile = TestUtils.createTempFile(PATH, "gene_sets.gmt").getAbsolutePath();
    String expressionFile = TestUtils.createTempFile(PATH, "FakeExpression.txt").getAbsolutePath();
    String enrichmentFile = TestUtils.createTempFile(PATH, "fakeEnrichments.txt").getAbsolutePath();
    String rankFile = TestUtils.createTempFile(PATH, "FakeRank.rnk").getAbsolutePath();
    PropertyManager pm = new PropertyManager();
    EMCreationParameters params = new EMCreationParameters("EM1_", pm.getDefaultPvalue(), pm.getDefaultQvalue(), NESFilter.ALL, Optional.empty(), SimilarityMetric.JACCARD, pm.getDefaultJaccardCutOff(), pm.getDefaultCombinedConstant());
    DataSetFiles dataset1files = new DataSetFiles();
    dataset1files.setGMTFileName(geneSetsFile);
    dataset1files.setExpressionFileName(expressionFile);
    dataset1files.setEnrichmentFileName1(enrichmentFile);
    dataset1files.setRankedFile(rankFile);
    buildEnrichmentMap(params, dataset1files, LegacySupport.DATASET1);
    // Assert the network is as expected
    Set<CyNetwork> networks = networkManager.getNetworkSet();
    assertEquals(1, networks.size());
    CyNetwork network = networks.iterator().next();
    Map<String, CyNode> nodes = TestUtils.getNodes(network);
    assertEquals(4, nodes.size());
    assertTrue(nodes.containsKey("BOTTOM8_PLUS100"));
    assertTrue(nodes.containsKey("MIDDLE8_PLUS100"));
    assertTrue(nodes.containsKey("TOP8_PLUS100"));
    assertTrue(nodes.containsKey("TOP1_PLUS100"));
    EdgeSimilarities edges = TestUtils.getEdgeSimilarities(network);
    assertEquals(6, edges.size());
    assertTrue(edges.containsEdge("MIDDLE8_PLUS100", "Geneset_Overlap", "BOTTOM8_PLUS100"));
    assertTrue(edges.containsEdge("TOP8_PLUS100", "Geneset_Overlap", "MIDDLE8_PLUS100"));
    assertTrue(edges.containsEdge("TOP8_PLUS100", "Geneset_Overlap", "BOTTOM8_PLUS100"));
    assertTrue(edges.containsEdge("TOP1_PLUS100", "Geneset_Overlap", "TOP8_PLUS100"));
    assertTrue(edges.containsEdge("TOP1_PLUS100", "Geneset_Overlap", "MIDDLE8_PLUS100"));
    assertTrue(edges.containsEdge("TOP1_PLUS100", "Geneset_Overlap", "BOTTOM8_PLUS100"));
}

Example 8 with CyNetwork

use of org.cytoscape.model.CyNetwork in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method reset.

public void reset() {
    invokeOnEDT(() -> {
        updating = true;
        try {
            for (CyNetworkView view : networkViewManager.getNetworkViewSet()) getControlPanel().removeEnrichmentMapView(view);
            Map<Long, EnrichmentMap> maps = emManager.getAllEnrichmentMaps();
            for (EnrichmentMap map : maps.values()) {
                CyNetwork network = networkManager.getNetwork(map.getNetworkID());
                Collection<CyNetworkView> networkViews = networkViewManager.getNetworkViews(network);
                for (CyNetworkView netView : networkViews) addNetworkView(netView);
            }
        } finally {
            updating = false;
        }
        setCurrentNetworkView(applicationManager.getCurrentNetworkView());
    });
}

Example 9 with CyNetwork

use of org.cytoscape.model.CyNetwork in project EnrichmentMapApp by BaderLab.

the class ChartUtil method calculateGlobalRange.

/**
	 * @return List whose first item is the minimum value of the range, and whose second item is the maximum value.
	 */
@SuppressWarnings("unchecked")
public static List<Double> calculateGlobalRange(CyNetwork network, List<CyColumnIdentifier> dataColumns) {
    List<Double> range = new ArrayList<>(2);
    List<CyNode> nodes = network.getNodeList();
    if (!nodes.isEmpty()) {
        double min = Double.POSITIVE_INFINITY;
        double max = Double.NEGATIVE_INFINITY;
        Collection<CyColumn> columns = network.getDefaultNodeTable().getColumns();
        Map<String, CyColumn> columnMap = columns.stream().collect(Collectors.toMap(CyColumn::getName, c -> c));
        for (final CyColumnIdentifier colId : dataColumns) {
            final CyColumn column = columnMap.get(colId.getColumnName());
            if (column == null)
                continue;
            final Class<?> colType = column.getType();
            final Class<?> colListType = column.getListElementType();
            if (Number.class.isAssignableFrom(colType) || (List.class.isAssignableFrom(colType) && Number.class.isAssignableFrom(colListType))) {
                for (final CyNode n : nodes) {
                    List<? extends Number> values = null;
                    final CyRow row = network.getRow(n);
                    if (List.class.isAssignableFrom(colType))
                        values = (List<? extends Number>) row.getList(column.getName(), colListType);
                    else if (row.isSet(column.getName()))
                        values = Collections.singletonList((Number) row.get(column.getName(), colType));
                    double[] mm = minMax(min, max, values);
                    min = mm[0];
                    max = mm[1];
                }
            }
        }
        if (min != Double.POSITIVE_INFINITY && max != Double.NEGATIVE_INFINITY) {
            range.add(min);
            range.add(max);
        }
    } else {
        range.add(0d);
        range.add(0d);
    }
    return range;
}

Example 10 with CyNetwork

use of org.cytoscape.model.CyNetwork in project EnrichmentMapApp by BaderLab.

the class FilterNodesEdgesTask method filterEdges.

private void filterEdges(Set<CyNode> nodes, Set<CyEdge> edges, TaskMonitor taskMonitor, double initialProgress) {
    CyNetwork net = networkView.getModel();
    List<CyEdge> edgeList = net.getEdgeList();
    int total = edgeList.size();
    int count = 0;
    float progress = (float) initialProgress;
    for (CyEdge e : edgeList) {
        if (cancelled)
            return;
        final View<CyEdge> ev = networkView.getEdgeView(e);
        if (ev == null)
            // Should never happen!
            continue;
        boolean filteredIn = edges.contains(e) && nodes.contains(e.getSource()) && nodes.contains(e.getTarget());
        // Don't forget to remove all locked values first!
        ev.clearValueLock(EDGE_VISIBLE);
        ev.clearValueLock(EDGE_TRANSPARENCY);
        ev.clearValueLock(EDGE_LABEL_TRANSPARENCY);
        if (filteredIn) {
            if (filterMode == FilterMode.SELECT)
                net.getRow(e).set(CyNetwork.SELECTED, true);
        } else {
            switch(filterMode) {
                case HIDE:
                    net.getRow(e).set(CyNetwork.SELECTED, false);
                    ev.setLockedValue(EDGE_VISIBLE, false);
                    break;
                case HIGHLIGHT:
                    ev.setLockedValue(EDGE_TRANSPARENCY, FILTERED_OUT_EDGE_TRANSPARENCY);
                    ev.setLockedValue(EDGE_LABEL_TRANSPARENCY, FILTERED_OUT_EDGE_TRANSPARENCY);
                    break;
                case SELECT:
                    net.getRow(e).set(CyNetwork.SELECTED, false);
                    break;
            }
        }
        // Use only 2 decimals to avoid too many UI updates when setting very small numbers
        float newProgress = Math.round((initialProgress + count * (1 - initialProgress) / total) * 100) / 100.0f;
        if (newProgress != progress) {
            taskMonitor.setProgress(newProgress);
            progress = newProgress;
        }
        count++;
    }
}