Examples with EnrichmentMap org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap used on opensource projects

Example 21 with EnrichmentMap

use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap in project EnrichmentMapApp by BaderLab.

the class LegacySessionLoadTest method getEnrichmentMap.

private EnrichmentMap getEnrichmentMap() {
    EnrichmentMapManager emManager = injector.getInstance(EnrichmentMapManager.class);
    Map<Long, EnrichmentMap> maps = emManager.getAllEnrichmentMaps();
    assertEquals(1, maps.size());
    EnrichmentMap map = maps.values().iterator().next();
    return map;
}

Example 22 with EnrichmentMap

use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap 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 23 with EnrichmentMap

use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap in project EnrichmentMapApp by BaderLab.

the class ControlPanel method updateEmViewCombo.

void updateEmViewCombo() {
    CyNetworkView selectedItem = (CyNetworkView) getEmViewCombo().getSelectedItem();
    Map<Long, EnrichmentMap> emMap = emManager.getAllEnrichmentMaps();
    getEmViewCombo().setEnabled(!emMap.isEmpty());
    getEmViewCombo().removeAllItems();
    if (!emMap.isEmpty()) {
        Set<CyNetworkView> allViews = networkViewManager.getNetworkViewSet();
        List<CyNetworkView> emViews = allViews.stream().filter(emManager::isEnrichmentMap).collect(Collectors.toList());
        Collator collator = Collator.getInstance(Locale.getDefault());
        emViews.sort((v1, v2) -> collator.compare(NetworkUtil.getTitle(v1), NetworkUtil.getTitle(v2)));
        emViews.forEach(getEmViewCombo()::addItem);
        getEmViewCombo().setSelectedItem(selectedItem);
    }
}

Example 24 with EnrichmentMap

use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap in project EnrichmentMapApp by BaderLab.

the class ControlPanel method update.

void update(CyNetworkView currentView) {
    // Is there an EnrichmentMap for this view?
    EnrichmentMap em = currentView != null ? emManager.getEnrichmentMap(currentView.getModel().getSUID()) : null;
    if (em == null)
        // This view is not an EnrichmentMap one!
        currentView = null;
    updateEmViewComboSelection(currentView);
    showViewControlPanel(currentView);
}

Example 25 with EnrichmentMap

use of org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap 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());
    });
}