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

Example 16 with EMDataSet

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

the class FileReaderTest method testGenericFileReader_5columns.

@Test
public void testGenericFileReader_5columns(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test expression file
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/generic_enr_5col.txt";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set enrichment results file name
    params.getFiles().get(LegacySupport.DATASET1).setEnrichmentFileName1(testDataFileName);
    //Create a new Enrichment map
    EnrichmentMap map = new EnrichmentMap(params.getCreationParameters(), serviceRegistrar);
    //get the default dataset
    Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
    DataSetFiles files = params.getFiles().get(LegacySupport.DATASET1);
    EMDataSet dataset = map.createDataSet(LegacySupport.DATASET1, method, files);
    // check if empty
    assertEquals(0, map.getDataSet(LegacySupport.DATASET1).getEnrichments().getEnrichments().size());
    // read
    ParseGenericEnrichmentResults task = new ParseGenericEnrichmentResults(dataset);
    task.run(taskMonitor);
    Map<String, EnrichmentResult> results = map.getDataSet(LegacySupport.DATASET1).getEnrichments().getEnrichments();
    // check we have 4 results
    assertEquals(4, results.size());
    // check pValues
    assertEquals(0.01, ((GenericResult) results.get("GO:0000346")).getPvalue(), 0.0);
    assertEquals(0.05, ((GenericResult) results.get("GO:0030904")).getPvalue(), 0.0);
    assertEquals(0.05, ((GenericResult) results.get("GO:0008623")).getPvalue(), 0.0);
    assertEquals(5.60E-42, ((GenericResult) results.get("GO:0046540")).getPvalue(), 0.0);
    // check getFdrqvalues
    assertEquals(0.02, ((GenericResult) results.get("GO:0000346")).getFdrqvalue(), 0.0);
    assertEquals(0.10, ((GenericResult) results.get("GO:0030904")).getFdrqvalue(), 0.0);
    assertEquals(0.12, ((GenericResult) results.get("GO:0008623")).getFdrqvalue(), 0.0);
    assertEquals(0.03, ((GenericResult) results.get("GO:0046540")).getFdrqvalue(), 0.0);
    // check phenotypes
    assertEquals(1.0, ((GenericResult) results.get("GO:0000346")).getNES(), 0.0);
    assertEquals(1.0, ((GenericResult) results.get("GO:0030904")).getNES(), 0.0);
    assertEquals(-1.0, ((GenericResult) results.get("GO:0008623")).getNES(), 0.0);
    assertEquals(-1.0, ((GenericResult) results.get("GO:0046540")).getNES(), 0.0);
    return;
}

Example 17 with EMDataSet

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

the class FileReaderTest method testGSEAEDBEnrichmentsReader.

//test GSEA enrichment results reader
@Test
public void testGSEAEDBEnrichmentsReader(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test enrichment files - GSEA creates two enrichment results files.
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/LoadDataset/GSEA_example_results/edb/results.edb";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set enrichment file name 
    params.getFiles().get(LegacySupport.DATASET1).setEnrichmentFileName1(testDataFileName);
    //Create a new Enrichment map
    EnrichmentMap map = new EnrichmentMap(params.getCreationParameters(), serviceRegistrar);
    //get the default dataset
    Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
    DataSetFiles files = params.getFiles().get(LegacySupport.DATASET1);
    EMDataSet dataset = map.createDataSet(LegacySupport.DATASET1, method, files);
    ParseEDBEnrichmentResults task = new ParseEDBEnrichmentResults(dataset);
    task.run(taskMonitor);
    //Get the enrichment
    Map<String, EnrichmentResult> enrichments = map.getDataSet(LegacySupport.DATASET1).getEnrichments().getEnrichments();
    assertEquals(14, enrichments.size());
    //Check the contents of some of the genesets
    // example from file 1 (ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612)
    //check p-values
    assertEquals(0.2271, ((GSEAResult) enrichments.get("PROTEASOME ACTIVATOR COMPLEX%GO%GO:0008537")).getPvalue(), 0.0);
    //check fdr value
    assertEquals(0.2447, ((GSEAResult) enrichments.get("PROTEASOME ACTIVATOR COMPLEX%GO%GO:0008537")).getFdrqvalue(), 0.0);
    //check ES value
    assertEquals(0.7852, ((GSEAResult) enrichments.get("PROTEASOME ACTIVATOR COMPLEX%GO%GO:0008537")).getES(), 0.0);
    //check NES
    assertEquals(1.1793, ((GSEAResult) enrichments.get("PROTEASOME ACTIVATOR COMPLEX%GO%GO:0008537")).getNES(), 0.0);
    //check ranks at max
    assertEquals(6, ((GSEAResult) enrichments.get("PROTEASOME ACTIVATOR COMPLEX%GO%GO:0008537")).getRankAtMax());
    //check size
    assertEquals(2, ((GSEAResult) enrichments.get("PROTEASOME ACTIVATOR COMPLEX%GO%GO:0008537")).getGsSize());
    // example from file 2 (EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143)
    //check p-values
    assertEquals(0.4545, ((GSEAResult) enrichments.get("PROTEASOME COMPLEX%GO%GO:0000502")).getPvalue(), 0.0);
    //check fdr value
    assertEquals(0.8650, ((GSEAResult) enrichments.get("PROTEASOME COMPLEX%GO%GO:0000502")).getFdrqvalue(), 0.0);
    //check ES value
    assertEquals(-0.4707, ((GSEAResult) enrichments.get("PROTEASOME COMPLEX%GO%GO:0000502")).getES(), 0.0);
    //check NES
    assertEquals(-0.9696, ((GSEAResult) enrichments.get("PROTEASOME COMPLEX%GO%GO:0000502")).getNES(), 0.0);
    //check ranks at max
    //The Rank at max in the edb file is different from the excel files.  In the excel file that we have been
    //  using up until now they convert the rank as if you are counting from the bottom of the list but in the 
    //edb file they count from the top of the ranked list (going from positive to negative ES scores)
    assertEquals(15, ((GSEAResult) enrichments.get("PROTEASOME COMPLEX%GO%GO:0000502")).getRankAtMax());
    //check size
    assertEquals(39, ((GSEAResult) enrichments.get("PROTEASOME COMPLEX%GO%GO:0000502")).getGsSize());
}

Example 18 with EMDataSet

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

the class BaseNetworkTest method runPostAnalysis.

protected void runPostAnalysis(CyNetwork emNetwork, PostAnalysisParameters.Builder builder, String dataSetName) throws Exception {
    // Set up mocks
    when(applicationManager.getCurrentNetwork()).thenReturn(emNetwork);
    CyNetworkView networkViewMock = mock(CyNetworkView.class);
    when(applicationManager.getCurrentNetworkView()).thenReturn(networkViewMock);
    when(networkViewManager.getNetworkViews(emNetwork)).thenReturn(Arrays.asList(networkViewMock));
    @SuppressWarnings("unchecked") View<CyNode> nodeViewMock = Mockito.mock(View.class);
    when(networkViewMock.getNodeView(Matchers.<CyNode>anyObject())).thenReturn(nodeViewMock);
    when(nodeViewMock.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION)).thenReturn(Double.valueOf(0.0));
    EnrichmentMap map = emManager.getEnrichmentMap(emNetwork.getSUID());
    assertNotNull(map);
    // Load the gene-sets from the file
    SerialTestTaskManager testTaskManager = new SerialTestTaskManager();
    File file = new File(builder.getSignatureGMTFileName());
    LoadSignatureSetsActionListener loader = loadSignatureSetsActionListenerFactory.create(file, new FilterMetric.None(), map);
    loader.setTaskManager(testTaskManager);
    loader.setGeneSetCallback(builder::setLoadedGMTGeneSets);
    loader.setFilteredSignatureSetsCallback(builder::addSelectedGeneSetNames);
    loader.actionPerformed(null);
    PostAnalysisParameters paParams = builder.build();
    // Run post-analysis
    EMDataSet dataSet = map.getDataSet(dataSetName);
    CreateDiseaseSignatureTaskParallel signatureTask = buildDiseaseSignatureTaskFactory.create(paParams, map, Arrays.asList(dataSet));
    testTaskManager = new SerialTestTaskManager();
    testTaskManager.execute(new TaskIterator(signatureTask));
}

Example 19 with EMDataSet

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

the class LoadBingoResultsTest method testLoad2BingoResult_withoutexpression.

@Test
public void testLoad2BingoResult_withoutexpression() throws Exception {
    //for a dataset we require genesets, an expression file (optional), enrichment results
    String testBingoResultsFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/bingo_output/12Hr_topgenes.bgo";
    DataSetFiles files = new DataSetFiles();
    files.setEnrichmentFileName1(testBingoResultsFileName);
    //for a dataset we require genesets, an expression file (optional), enrichment results
    String testBingoResultsFileName2 = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/bingo_output/24Hr_topgenes.bgo";
    DataSetFiles files2 = new DataSetFiles();
    files2.setEnrichmentFileName1(testBingoResultsFileName2);
    //set the method to Bingo
    double pvalue = 0.00005;
    // 5.0 X 10-8
    double qvaule = 0.00000005;
    double similarityCutoff = 0.25;
    EMCreationParameters params = new EMCreationParameters("EM1_", pvalue, qvaule, NESFilter.ALL, Optional.empty(), SimilarityMetric.JACCARD, similarityCutoff, 0.5);
    //create an new enrichment Map
    EnrichmentMap em = new EnrichmentMap(params, serviceRegistrar);
    EMDataSet dataset = em.createDataSet(LegacySupport.DATASET1, Method.Specialized, files);
    ParseBingoEnrichmentResults enrichmentResultsFilesTask = new ParseBingoEnrichmentResults(dataset);
    enrichmentResultsFilesTask.run(taskMonitor);
    //Load second dataset
    //create a dataset
    EMDataSet dataset2 = em.createDataSet(LegacySupport.DATASET2, Method.Specialized, files2);
    //create a DatasetTask
    ParseBingoEnrichmentResults enrichmentResultsFiles2Task = new ParseBingoEnrichmentResults(dataset2);
    enrichmentResultsFiles2Task.run(taskMonitor);
    CreateDummyExpressionTask dummyExpressionTask = new CreateDummyExpressionTask(dataset);
    dummyExpressionTask.run(taskMonitor);
    CreateDummyExpressionTask dummyExpressionTask2 = new CreateDummyExpressionTask(dataset2);
    dummyExpressionTask2.run(taskMonitor);
    //check to see if the two datasets are distinct
    if (!((dataset.getDataSetGenes().containsAll(dataset2.getDataSetGenes())) && (dataset2.getDataSetGenes().containsAll(dataset.getDataSetGenes()))))
        em.setDistinctExpressionSets(true);
    em.filterGenesets();
    InitializeGenesetsOfInterestTask genesets_init = new InitializeGenesetsOfInterestTask(em);
    genesets_init.run(taskMonitor);
    //		ComputeSimilarityTask similarities = new ComputeSimilarityTask(em);
    //		similarities.run(taskMonitor);
    dataset = em.getDataSet(LegacySupport.DATASET1);
    //get the stats for the first dataset		
    //check to see if the dataset loaded - there should be 74 genesets
    assertEquals(74, dataset.getSetOfGeneSets().getGeneSets().size());
    //there should also be 74 enrichments (the genesets are built from the bgo file)
    assertEquals(74, dataset.getEnrichments().getEnrichments().size());
    //there should be 11 genesets in the enrichments of interest
    assertEquals(5, dataset.getGeneSetsOfInterest().getGeneSets().size());
    //there should be 43 genes in the geneset "nucleolus"
    assertEquals(43, dataset.getSetOfGeneSets().getGeneSets().get("NUCLEOLUS").getGenes().size());
    //make sure the dummy expression has values for all the genes
    assertEquals(446, dataset.getExpressionSets().getNumGenes());
    assertEquals(446, dataset.getDataSetGenes().size());
    dataset2 = em.getDataSet(LegacySupport.DATASET2);
    //check the stats for dataset2
    //check to see if the dataset loaded - there should be 74 genesets
    assertEquals(87, dataset2.getSetOfGeneSets().getGeneSets().size());
    //there should also be 74 enrichments (the genesets are built from the bgo file)
    assertEquals(87, dataset2.getEnrichments().getEnrichments().size());
    //there should be 11 genesets in the enrichments of interest
    assertEquals(2, dataset2.getGeneSetsOfInterest().getGeneSets().size());
    //there should be 43 genes in the geneset "nucleolus"
    assertEquals(318, dataset2.getSetOfGeneSets().getGeneSets().get("INTRACELLULAR").getGenes().size());
    //make sure the dummy expression has values for all the genes
    assertEquals(398, dataset2.getExpressionSets().getNumGenes());
    assertEquals(398, dataset2.getDataSetGenes().size());
    //there should be 20 edges (2 edges for every node because of the distinct expresison sets)
    //assertEquals(24,em.getGenesetSimilarity().size());
    //there should be a total of 366 genes
    assertEquals(704, em.getNumberOfGenes());
}

Example 20 with EMDataSet

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

the class LoadEdbDatasetTest method testEdbLoad.

@Test
public void testEdbLoad() throws Exception {
    //for a dataset we require genesets, an expression file (optional), enrichment results
    String testEdbResultsFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/LoadDataset/GSEA_example_results/edb/results.edb";
    String testgmtFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/LoadDataset/GSEA_example_results/edb/gene_sets.gmt";
    String testrnkFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/LoadDataset/GSEA_example_results/edb/Expressionfile.rnk";
    DataSetFiles files = new DataSetFiles();
    files.setEnrichmentFileName1(testEdbResultsFileName);
    files.setGMTFileName(testgmtFileName);
    files.setRankedFile(testrnkFileName);
    //set the method to gsea
    double similarityCutoff = 0.5;
    double pvalue = 1.0;
    double qvalue = 1.0;
    EMCreationParameters params = new EMCreationParameters("EM1_", pvalue, qvalue, NESFilter.ALL, Optional.empty(), SimilarityMetric.JACCARD, similarityCutoff, 0.5);
    //create an new enrichment Map
    EnrichmentMap em = new EnrichmentMap(params, serviceRegistrar);
    //Load data set
    //create a dataset
    EMDataSet dataset = em.createDataSet(LegacySupport.DATASET1, Method.GSEA, files);
    //create a DatasetTask
    //create a DatasetTask
    //load Data
    GMTFileReaderTask task = new GMTFileReaderTask(dataset);
    task.run(taskMonitor);
    ParseEDBEnrichmentResults enrichmentResultsFilesTask = new ParseEDBEnrichmentResults(dataset);
    enrichmentResultsFilesTask.run(taskMonitor);
    //create dummy expression
    CreateDummyExpressionTask dummyExpressionTask = new CreateDummyExpressionTask(dataset);
    dummyExpressionTask.run(taskMonitor);
    em.filterGenesets();
    InitializeGenesetsOfInterestTask genesets_init = new InitializeGenesetsOfInterestTask(em);
    genesets_init.run(taskMonitor);
    //check to see if the dataset loaded
    //although the original analysis had 193 genesets because this is loaded from
    //edb version it only stores the genesets that overlapped with the dataset analyzed.
    assertEquals(14, dataset.getSetOfGeneSets().getGeneSets().size());
    assertEquals(14, dataset.getEnrichments().getEnrichments().size());
    assertEquals(41, dataset.getDataSetGenes().size());
    assertEquals(41, dataset.getExpressionSets().getNumGenes());
}