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

Example 1 with CyEdge

use of org.cytoscape.model.CyEdge 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++;
    }
}

Example 2 with CyEdge

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

the class CreateEMNetworkTask method createEdges.

/**
	 * Note, we expect that GenesetSimilarity object that don't pass the cutoff have already been filtered out.
	 * @param network
	 * @param nodes
	 */
private void createEdges(CyNetwork network, Map<String, CyNode> nodes) {
    Map<SimilarityKey, GenesetSimilarity> similarities = supplier.get();
    for (SimilarityKey key : similarities.keySet()) {
        GenesetSimilarity similarity = similarities.get(key);
        CyNode node1 = nodes.get(similarity.getGeneset1Name());
        CyNode node2 = nodes.get(similarity.getGeneset2Name());
        CyEdge edge = network.addEdge(node1, node2, false);
        String datasetName = key.getName();
        if (datasetName != null) {
            EMDataSet dataset = map.getDataSet(datasetName);
            if (dataset != null) {
                dataset.addEdgeSuid(edge.getSUID());
            }
        }
        List<String> overlapGenes = similarity.getOverlappingGenes().stream().map(map::getGeneFromHashKey).collect(Collectors.toList());
        String edgeName = key.toString();
        CyRow row = network.getRow(edge);
        row.set(CyNetwork.NAME, edgeName);
        row.set(CyEdge.INTERACTION, similarity.getInteractionType());
        Columns.EDGE_SIMILARITY_COEFF.set(row, prefix, null, similarity.getSimilarityCoeffecient());
        Columns.EDGE_OVERLAP_SIZE.set(row, prefix, null, similarity.getSizeOfOverlap());
        Columns.EDGE_OVERLAP_GENES.set(row, prefix, null, overlapGenes);
        if (key.isCompound()) {
            Columns.EDGE_DATASET.set(row, prefix, null, Columns.EDGE_DATASET_VALUE_COMPOUND);
        } else {
            Columns.EDGE_DATASET.set(row, prefix, null, similarity.getDataSetName());
        }
    }
}

Example 3 with CyEdge

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

the class PostAnalysisTaskTest method test_2_PostAnalysisMannWhitney.

/**
	 * Run post-analysis with the default mann-whitney test.
	 * Uses the network that was created by the previous test method.
	 */
@Test
public void test_2_PostAnalysisMannWhitney(@Continuous VisualMappingFunctionFactory cmFactory) throws Exception {
    mockContinuousMappingFactory(cmFactory);
    PostAnalysisParameters.Builder builder = new PostAnalysisParameters.Builder();
    builder.setAnalysisType(AnalysisType.KNOWN_SIGNATURE);
    builder.setUniverseType(UniverseType.USER_DEFINED);
    builder.setUserDefinedUniverseSize(11445);
    builder.setSignatureGMTFileName(PATH + "PA_top8_middle8_bottom8.gmt");
    builder.setAttributePrefix("EM1_");
    builder.addDataSetToRankFile(LegacySupport.DATASET1, LegacySupport.DATASET1);
    PostAnalysisFilterParameters rankTest = new PostAnalysisFilterParameters(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED);
    builder.setRankTestParameters(rankTest);
    runPostAnalysis(emNetwork, builder, LegacySupport.DATASET1);
    // Assert that post-analysis created the new nodes correctly
    Map<String, CyNode> nodes = TestUtils.getNodes(emNetwork);
    assertEquals(5, nodes.size());
    assertTrue(nodes.containsKey("PA_TOP8_MIDDLE8_BOTTOM8"));
    EdgeSimilarities edges = TestUtils.getEdgeSimilarities(emNetwork);
    assertEquals(8, edges.size());
    CyEdge edge1 = edges.getEdge("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) TOP8_PLUS100");
    assertNotNull(edge1);
    assertEquals(1.40E-6, emNetwork.getRow(edge1).get("EM1_Overlap_Mann_Whit_pVal", Double.class), 0.001);
    assertEquals(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED.toString(), emNetwork.getRow(edge1).get("EM1_Overlap_cutoff", String.class));
    CyEdge edge2 = edges.getEdge("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) BOTTOM8_PLUS100");
    assertNotNull(edge2);
    assertEquals(1.40E-6, emNetwork.getRow(edge2).get("EM1_Overlap_Mann_Whit_pVal", Double.class), 0.001);
    assertEquals(PostAnalysisFilterType.MANN_WHIT_TWO_SIDED.toString(), emNetwork.getRow(edge2).get("EM1_Overlap_cutoff", String.class));
}

Example 4 with CyEdge

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

the class PostAnalysisTaskTest method test_4_WidthFunction.

@Test
public void test_4_WidthFunction(@Continuous VisualMappingFunctionFactory cmFactory, EnrichmentMapManager emManager, Provider<WidthFunction> widthFunctionProvider) {
    CyNetworkManager networkManager = mock(CyNetworkManager.class);
    when(networkManager.getNetworkSet()).thenReturn(Collections.singleton(emNetwork));
    mockContinuousMappingFactory(cmFactory);
    EdgeSimilarities edges = TestUtils.getEdgeSimilarities(emNetwork);
    CyEdge sigEdge1 = edges.getEdge("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) TOP8_PLUS100");
    CyEdge sigEdge2 = edges.getEdge("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) TOP1_PLUS100");
    EnrichmentMap map = emManager.getEnrichmentMap(emNetwork.getSUID());
    assertNotNull(map);
    WidthFunction widthFunction = widthFunctionProvider.get();
    widthFunction.setEdgeWidths(emNetwork, "EM1_", null);
    String widthCol = Columns.EDGE_WIDTH_FORMULA_COLUMN.with("EM1_", null);
    double sigWidth1 = emNetwork.getRow(sigEdge1).get(widthCol, Double.class);
    assertEquals(8.0, sigWidth1, 0.0);
    double sigWidth2 = emNetwork.getRow(sigEdge2).get(widthCol, Double.class);
    assertEquals(1.0, sigWidth2, 0.0);
}

Example 5 with CyEdge

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

the class PostAnalysisCutoffTest method test_1_FilterType_Number.

@Test
public void test_1_FilterType_Number(@Continuous VisualMappingFunctionFactory cmFactory) throws Exception {
    mockContinuousMappingFactory(cmFactory);
    PostAnalysisParameters.Builder builder = getBuilder();
    PostAnalysisFilterParameters rankTest = new PostAnalysisFilterParameters(PostAnalysisFilterType.NUMBER, 5);
    builder.setRankTestParameters(rankTest);
    runPostAnalysis(emNetwork, builder, LegacySupport.DATASET1);
    Map<String, CyEdge> edges = TestUtils.getEdges(emNetwork);
    assertEquals(9, edges.size());
    CyEdge edge = edges.get("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) MIDDLE8_PLUS100");
    assertNotNull(edge);
    assertEquals(8, emNetwork.getRow(edge).get("EM1_k_intersection", Integer.class).intValue());
    assertEquals(PostAnalysisFilterType.NUMBER.toString(), emNetwork.getRow(edge).get("EM1_Overlap_cutoff", String.class));
    edge = edges.get("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) BOTTOM8_PLUS100");
    assertNotNull(edge);
    assertEquals(8, emNetwork.getRow(edge).get("EM1_k_intersection", Integer.class).intValue());
    assertEquals(PostAnalysisFilterType.NUMBER.toString(), emNetwork.getRow(edge).get("EM1_Overlap_cutoff", String.class));
    edge = edges.get("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) TOP8_PLUS100");
    assertNotNull(edge);
    assertEquals(8, emNetwork.getRow(edge).get("EM1_k_intersection", Integer.class).intValue());
    assertEquals(PostAnalysisFilterType.NUMBER.toString(), emNetwork.getRow(edge).get("EM1_Overlap_cutoff", String.class));
    edge = edges.get("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) TOP1_PLUS100");
    assertNull(edge);
}