Examples with ParseBingoEnrichmentResults org.baderlab.csplugins.enrichmentmap.parsers.ParseBingoEnrichmentResults used on opensource projects

Example 1 with ParseBingoEnrichmentResults

use of org.baderlab.csplugins.enrichmentmap.parsers.ParseBingoEnrichmentResults 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 2 with ParseBingoEnrichmentResults

use of org.baderlab.csplugins.enrichmentmap.parsers.ParseBingoEnrichmentResults in project EnrichmentMapApp by BaderLab.

the class LoadBingoResultsTest method testLoadBingoResult_withoutexpression.

@Test
public void testLoadBingoResult_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);
    //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);
    CreateDummyExpressionTask dummyExpressionTask = new CreateDummyExpressionTask(dataset);
    dummyExpressionTask.run(taskMonitor);
    em.filterGenesets();
    InitializeGenesetsOfInterestTask genesets_init = new InitializeGenesetsOfInterestTask(em);
    genesets_init.run(taskMonitor);
    Baton<Map<SimilarityKey, GenesetSimilarity>> baton = new Baton<>();
    ComputeSimilarityTaskParallel similarities = new ComputeSimilarityTaskParallel(em, baton.consumer());
    similarities.run(taskMonitor);
    //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 6 edges
    assertEquals(6, baton.supplier().get().size());
    //there should be a total of 366 genes
    assertEquals(446, em.getNumberOfGenes());
    //there should be 43 genes in the geneset "nucleolus"
    assertEquals(43, em.getAllGeneSets().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());
}