Examples with Baton org.baderlab.csplugins.enrichmentmap.util.Baton used on opensource projects

Example 1 with Baton

use of org.baderlab.csplugins.enrichmentmap.util.Baton in project EnrichmentMapApp by BaderLab.

the class GeneSetSimilarityTest method testCombindCalculations.

@Test
public void testCombindCalculations() throws Exception {
    double combined_constant = 0.5;
    //set the parameters in the params to use jaccard coeffecient calculation
    map.getParams().setSimilarityMetric(EMCreationParameters.SimilarityMetric.COMBINED);
    //set the cutoff to the max
    map.getParams().setSimilarityCutoff(0);
    map.getParams().setCombinedConstant(combined_constant);
    Baton<Map<SimilarityKey, GenesetSimilarity>> baton = new Baton<>();
    ComputeSimilarityTaskParallel sim_task = new ComputeSimilarityTaskParallel(map, baton.consumer());
    sim_task.run(taskMonitor);
    Map<SimilarityKey, GenesetSimilarity> similarities = baton.supplier().get();
    assertEquals(15, similarities.size());
    //SetOfGeneSets gs_set = map.getDataset(EnrichmentMap.DATASET1).getSetofgenesets();
    //check the gene set similarity between APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4
    //and APOPTOSIS%REACTOME%REACT_578.5
    GenesetSimilarity similarity;
    // Set A has 13 elements, Set B has 142 elements, They have 13 elements in common
    Double combined = (combined_constant * (13.0 / 13.0)) + ((1 - combined_constant) * (13.0 / 142.0));
    similarity = similarities.get(new SimilarityKey("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", "APOPTOSIS%REACTOME%REACT_578.5", "Geneset_Overlap", null));
    assertEquals(combined, similarity.getSimilarityCoeffecient(), 0.0);
    assertEquals(13, similarity.getSizeOfOverlap());
    if ("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4".equals(similarity.getGeneset1Name())) {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset1Name());
        assertEquals("APOPTOSIS%REACTOME%REACT_578.5", similarity.getGeneset2Name());
    } else {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset2Name());
        assertEquals("APOPTOSIS%REACTOME%REACT_578.5", similarity.getGeneset1Name());
    }
    // Set A has 13 elements, Set B has 9 elements, They have 1 elements in common
    combined = (combined_constant * (1.0 / 9.0)) + ((1 - combined_constant) * (1.0 / 21.0));
    similarity = similarities.get(new SimilarityKey("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", "APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS%REACTOME%REACT_13579.1", "Geneset_Overlap", null));
    assertEquals(combined, similarity.getSimilarityCoeffecient(), 0.0);
    assertEquals(1, similarity.getSizeOfOverlap());
    assertTrue(similarity.getOverlappingGenes().contains(map.getHashFromGene("CASP3")));
    if ("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4".equals(similarity.getGeneset1Name())) {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset1Name());
        assertEquals("APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS%REACTOME%REACT_13579.1", similarity.getGeneset2Name());
    } else {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset2Name());
        assertEquals("APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS%REACTOME%REACT_13579.1", similarity.getGeneset1Name());
    }
    // Set A has 13 elements, Set B has 7 elements, They have 1 elements in common
    combined = (combined_constant * (1.0 / 7.0)) + ((1 - combined_constant) * (1.0 / 19.0));
    ;
    similarity = similarities.get(new SimilarityKey("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", "APOPTOTIC FACTOR-MEDIATED RESPONSE%REACTOME%REACT_963.2", "Geneset_Overlap", null));
    assertEquals(combined, similarity.getSimilarityCoeffecient(), 0.0);
    assertEquals(1, similarity.getSizeOfOverlap());
    assertTrue(similarity.getOverlappingGenes().contains(map.getHashFromGene("CASP3")));
    if ("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4".equals(similarity.getGeneset1Name())) {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset1Name());
        assertEquals("APOPTOTIC FACTOR-MEDIATED RESPONSE%REACTOME%REACT_963.2", similarity.getGeneset2Name());
    } else {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset2Name());
        assertEquals("APOPTOTIC FACTOR-MEDIATED RESPONSE%REACTOME%REACT_963.2", similarity.getGeneset1Name());
    }
}

Example 2 with Baton

use of org.baderlab.csplugins.enrichmentmap.util.Baton in project EnrichmentMapApp by BaderLab.

the class GeneSetSimilarityTest method testJaccardCalculations.

@Test
public void testJaccardCalculations() throws Exception {
    //set the parameters in the params to use jaccard coeffecient calculation
    map.getParams().setSimilarityMetric(EMCreationParameters.SimilarityMetric.JACCARD);
    //set the cutoff to the max
    map.getParams().setSimilarityCutoff(0);
    Baton<Map<SimilarityKey, GenesetSimilarity>> baton = new Baton<>();
    ComputeSimilarityTaskParallel sim_task = new ComputeSimilarityTaskParallel(map, baton.consumer());
    sim_task.run(taskMonitor);
    Map<SimilarityKey, GenesetSimilarity> similarities = baton.supplier().get();
    assertEquals(15, similarities.size());
    //check the gene set similarity between APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4
    //and APOPTOSIS%REACTOME%REACT_578.5
    GenesetSimilarity similarity;
    // Set A has 13 elements, Set B has 142 elements, They have 13 elements in common
    Double jaccard = 13.0 / 142.0;
    similarity = similarities.get(new SimilarityKey("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", "APOPTOSIS%REACTOME%REACT_578.5", "Geneset_Overlap", null));
    assertEquals(jaccard, similarity.getSimilarityCoeffecient(), 0.0);
    assertEquals(13, similarity.getSizeOfOverlap());
    if (similarity.getGeneset1Name().equals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4")) {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset1Name());
        assertEquals("APOPTOSIS%REACTOME%REACT_578.5", similarity.getGeneset2Name());
    } else {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset2Name());
        assertEquals("APOPTOSIS%REACTOME%REACT_578.5", similarity.getGeneset1Name());
    }
    // Set A has 13 elements, Set B has 9 elements, They have 1 elements in common
    jaccard = 1.0 / 21.0;
    similarity = similarities.get(new SimilarityKey("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", "APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS%REACTOME%REACT_13579.1", "Geneset_Overlap", null));
    assertEquals(jaccard, similarity.getSimilarityCoeffecient(), 0.0);
    assertEquals(1, similarity.getSizeOfOverlap());
    assertTrue(similarity.getOverlappingGenes().contains(map.getHashFromGene("CASP3")));
    if ("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4".equals(similarity.getGeneset1Name())) {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset1Name());
        assertEquals("APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS%REACTOME%REACT_13579.1", similarity.getGeneset2Name());
    } else {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset2Name());
        assertEquals("APOPTOTIC CLEAVAGE OF CELL ADHESION PROTEINS%REACTOME%REACT_13579.1", similarity.getGeneset1Name());
    }
    // Set A has 13 elements, Set B has 7 elements, They have 1 elements in common
    jaccard = 1.0 / 19.0;
    similarity = similarities.get(new SimilarityKey("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", "APOPTOTIC FACTOR-MEDIATED RESPONSE%REACTOME%REACT_963.2", "Geneset_Overlap", null));
    assertEquals(jaccard, similarity.getSimilarityCoeffecient(), 0.0);
    assertEquals(1, similarity.getSizeOfOverlap());
    assertTrue(similarity.getOverlappingGenes().contains(map.getHashFromGene("CASP3")));
    if ("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4".equals(similarity.getGeneset1Name())) {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset1Name());
        assertEquals("APOPTOTIC FACTOR-MEDIATED RESPONSE%REACTOME%REACT_963.2", similarity.getGeneset2Name());
    } else {
        assertEquals("APOPTOSIS INDUCED DNA FRAGMENTATION%REACTOME%REACT_1213.4", similarity.getGeneset2Name());
        assertEquals("APOPTOTIC FACTOR-MEDIATED RESPONSE%REACTOME%REACT_963.2", similarity.getGeneset1Name());
    }
}

Example 3 with Baton

use of org.baderlab.csplugins.enrichmentmap.util.Baton in project EnrichmentMapApp by BaderLab.

the class CreateEnrichmentMapTaskFactory method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    TaskIterator tasks = new TaskIterator();
    if (dataSets.isEmpty())
        return tasks;
    tasks.append(new TitleTask("Building EnrichmentMap"));
    EnrichmentMap map = new EnrichmentMap(params, serviceRegistrar);
    for (DataSetParameters dataSetParameters : dataSets) {
        String datasetName = dataSetParameters.getName();
        Method method = dataSetParameters.getMethod();
        DataSetFiles files = dataSetParameters.getFiles();
        EMDataSet dataset = map.createDataSet(datasetName, method, files);
        // Load GMT File
        if (!Strings.isNullOrEmpty(dataset.getSetOfGeneSets().getFilename())) {
            tasks.append(new GMTFileReaderTask(dataset));
        }
        // Load the enrichments 
        tasks.append(new DetermineEnrichmentResultFileReader(dataset).getParsers());
        // If there is no expression file then create a dummy file to associate with this dataset so we can still use the expression viewer (heat map)
        if (Strings.isNullOrEmpty(dataset.getDataSetFiles().getExpressionFileName())) {
            tasks.append(new CreateDummyExpressionTask(dataset));
        } else {
            tasks.append(new ExpressionFileReaderTask(dataset));
        }
        // Load ranks if present
        String ranksName = dataset.getMethod() == Method.GSEA ? Ranking.GSEARanking : datasetName;
        if (dataset.getExpressionSets().getRanksByName(ranksName) != null) {
            String filename = dataset.getExpressionSets().getRanksByName(ranksName).getFilename();
            tasks.append(new RanksFileReaderTask(filename, dataset, ranksName, false));
        }
        if (!Strings.isNullOrEmpty(dataset.getDataSetFiles().getClassFile())) {
            tasks.append(new ClassFileReaderTask(dataset));
        }
    }
    // NOTE: First filter out genesets that don't pass the thresholds, 
    // Then filter the remaining genesets of interest to only contain genes from the expression file.
    // Filter out genesets that don't pass the p-value and q-value thresholds
    InitializeGenesetsOfInterestTask genesetsTask = new InitializeGenesetsOfInterestTask(map);
    //		genesetsTask.setThrowIfMissing(false); // TEMPORARY
    tasks.append(genesetsTask);
    // Trim the genesets to only contain the genes that are in the data file.
    tasks.append(new FilterGenesetsByDatasetGenes(map));
    // Link the ComputeSimilarityTask to the MasterMapNetworkTask by a "pipe"
    Baton<Map<SimilarityKey, GenesetSimilarity>> pipe = new Baton<>();
    // Compute the geneset similarities
    tasks.append(new ComputeSimilarityTaskParallel(map, pipe.consumer()));
    // Create the network
    tasks.append(createEMNetworkTaskFactory.create(map, pipe.supplier()));
    // Create style and layout
    if (!headless) {
        tasks.append(createEMViewTaskFactory.create(map));
    }
    return tasks;
}

Example 4 with Baton

use of org.baderlab.csplugins.enrichmentmap.util.Baton in project EnrichmentMapApp by BaderLab.

the class LoadGMTFileOnlyTest method testGMTOnly.

@Test
public void testGMTOnly() throws Exception {
    //for a dataset we require genesets, an expression file (optional), enrichment results
    String testGmtFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/task/genesets_subset.gmt";
    DataSetFiles files = new DataSetFiles();
    files.setGMTFileName(testGmtFileName);
    //create an new enrichment Map
    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);
    EnrichmentMap em = new EnrichmentMap(params, serviceRegistrar);
    //Load data set
    //create a dataset
    EMDataSet dataset = em.createDataSet(LegacySupport.DATASET1, Method.GSEA, files);
    //create a DatasetTask
    //set up task
    GMTFileReaderTask task = new GMTFileReaderTask(dataset);
    task.run(taskMonitor);
    dataset.setGeneSetsOfInterest(dataset.getSetOfGeneSets());
    //create dummy expression
    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 36 genesets
    assertEquals(36, dataset.getSetOfGeneSets().getGeneSets().size());
    //there should be (36 * 35)/2 edges (geneset similarities)
    assertEquals(18, baton.supplier().get().size());
    //there should be 523 genes
    assertEquals(523, em.getNumberOfGenes());
    assertEquals(523, dataset.getExpressionSets().getNumGenes());
    assertEquals(523, dataset.getDataSetGenes().size());
    assertEquals(3, dataset.getExpressionSets().getNumConditions());
}

Example 5 with Baton

use of org.baderlab.csplugins.enrichmentmap.util.Baton 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());
}