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

Example 6 with CyEdge

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

the class PostAnalysisCutoffTest method test_2_FilterType_Percent.

@Test
public void test_2_FilterType_Percent(@Continuous VisualMappingFunctionFactory cmFactory) throws Exception {
    mockContinuousMappingFactory(cmFactory);
    PostAnalysisParameters.Builder builder = getBuilder();
    PostAnalysisFilterParameters rankTest = new PostAnalysisFilterParameters(PostAnalysisFilterType.PERCENT, 7);
    builder.setRankTestParameters(rankTest);
    runPostAnalysis(emNetwork, builder, LegacySupport.DATASET1);
    assertEquals(12, emNetwork.getEdgeCount());
    Map<String, CyEdge> edges = TestUtils.getSignatureEdges(emNetwork, "EM1_", "PA_top8_middle8_bottom8(1)");
    assertEquals(3, 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.PERCENT.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.PERCENT.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.PERCENT.toString(), emNetwork.getRow(edge).get("EM1_Overlap_cutoff", String.class));
    edge = edges.get("PA_TOP8_MIDDLE8_BOTTOM8 (sig_Dataset 1) TOP1_PLUS100");
    assertNull(edge);
}

Example 7 with CyEdge

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

the class HeatMapMediator method getDataSetRankOptions.

private List<RankingOption> getDataSetRankOptions(EnrichmentMap map, CyNetwork network, List<CyNode> nodes, List<CyEdge> edges) {
    List<RankingOption> options = new ArrayList<>();
    for (EMDataSet dataset : map.getDataSetList()) {
        if (nodes.size() == 1 && edges.isEmpty() && dataset.getMethod() == Method.GSEA && contains(dataset, network, nodes.get(0))) {
            String geneSetName = network.getRow(nodes.get(0)).get(CyNetwork.NAME, String.class);
            Map<String, Ranking> ranks = dataset.getExpressionSets().getRanks();
            ranks.forEach((name, ranking) -> {
                options.add(new GSEALeadingEdgeRankingOption(dataset, geneSetName, name));
            });
        } else if (contains(network, dataset, nodes, edges)) {
            Map<String, Ranking> ranks = dataset.getExpressionSets().getRanks();
            ranks.forEach((name, ranking) -> {
                options.add(new BasicRankingOption(ranking, dataset, name));
            });
        }
    }
    return options;
}

Example 8 with CyEdge

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

the class HeatMapMediator method updateHeatMap.

private void updateHeatMap(CyNetworkView networkView) {
    if (heatMapPanel == null)
        return;
    CyNetwork network = networkView.getModel();
    EnrichmentMap map = emManager.getEnrichmentMap(network.getSUID());
    if (map == null)
        return;
    List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
    List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, true);
    String prefix = map.getParams().getAttributePrefix();
    this.onlyEdges = selectedNodes.isEmpty() && !selectedEdges.isEmpty();
    Set<String> union = unionGenesets(network, selectedNodes, selectedEdges, prefix);
    Set<String> inter = intersectionGenesets(network, selectedNodes, selectedEdges, prefix);
    List<RankingOption> rankOptions = getDataSetRankOptions(map, network, selectedNodes, selectedEdges);
    HeatMapParams params = getHeatMapParams(map, network.getSUID(), onlyEdges);
    heatMapPanel.selectGenes(map, params, rankOptions, union, inter);
}

Example 9 with CyEdge

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

the class HeatMapMediator method getDataSetRankOptions.

public List<RankingOption> getDataSetRankOptions(EnrichmentMap map) {
    CyNetwork network = networkManager.getNetwork(map.getNetworkID());
    List<CyNode> selectedNodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true);
    List<CyEdge> selectedEdges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, true);
    return getDataSetRankOptions(map, network, selectedNodes, selectedEdges);
}

Example 10 with CyEdge

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

the class HeatMapMediator method intersectionGenesets.

private static Set<String> intersectionGenesets(CyNetwork network, List<CyNode> nodes, List<CyEdge> edges, String prefix) {
    Set<String> inter = null;
    for (CyNode node : nodes) {
        Collection<String> genes = getGenes(network, node, prefix);
        if (inter == null)
            inter = new HashSet<>(genes);
        else
            inter.retainAll(genes);
    }
    for (CyEdge edge : edges) {
        Collection<String> genes = getGenes(network, edge.getSource(), prefix);
        if (inter == null)
            inter = new HashSet<>(genes);
        else
            inter.retainAll(genes);
        inter.retainAll(getGenes(network, edge.getTarget(), prefix));
    }
    return inter == null ? Collections.emptySet() : inter;
}