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

Example 16 with EnrichmentMap

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

the class HeatMapRanksTest method testLeadingEdge.

@Test
public void testLeadingEdge(EnrichmentMapManager emManager) throws Exception {
    final String geneSetName = "ENVELOPE%GO%GO:0031975";
    final int leadingEdgeSize = 170;
    // Sanity test
    EnrichmentMap map = emManager.getAllEnrichmentMaps().values().iterator().next();
    EMDataSet dataset = map.getDataSet(LegacySupport.DATASET1);
    GeneSet gs = dataset.getGeneSetsOfInterest().getGeneSets().get(geneSetName);
    assertNotNull(gs);
    // Run the ranking
    RankingOption rankingOption = new GSEALeadingEdgeRankingOption(dataset, geneSetName, Ranking.GSEARanking);
    Map<Integer, RankValue> ranks = rankingOption.computeRanking(gs.getGenes()).get().get();
    assertEquals(454, ranks.size());
    // Convert to useful collections
    Map<RankValue, Integer> rankToGeneId = HashBiMap.create(ranks).inverse();
    List<RankValue> sortedRanks = ranks.values().stream().sorted().collect(Collectors.toList());
    // Test leading edge
    for (int i = 0; i < sortedRanks.size(); i++) {
        RankValue v = sortedRanks.get(i);
        assertTrue(v.isSignificant() == i < leadingEdgeSize);
    }
    // Test genes are the same
    List<Integer> expectedGeneOrder = getGeneOrderFromFile(map, PATH + "gene_order_leading_edge.txt");
    List<Integer> actualGeneOrder = sortedRanks.stream().map(rankToGeneId::get).collect(Collectors.toList());
    assertEquals(expectedGeneOrder, actualGeneOrder);
}

Example 17 with EnrichmentMap

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

the class FileReaderTest method testExpression1ReaderRnk.

@Test
public void testExpression1ReaderRnk(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test expression file
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/ExpressionTestFile.rnk";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set expression file name 
    params.getFiles().get(LegacySupport.DATASET1).setExpressionFileName(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);
    //make sure that the genes are empty
    assertEquals(0, map.getNumberOfGenes());
    //add the gene to the master list of genes
    map.addGene("GLS");
    map.addGene("PSMA1");
    map.addGene("ZP1");
    map.addGene("ZYX");
    //make sure all four genes have been associated
    assertEquals(4, map.getNumberOfGenes());
    //load expression file
    ExpressionFileReaderTask task = new ExpressionFileReaderTask(dataset);
    task.run(taskMonitor);
    //There was one more gene in the expression file that wasn't in the set of genes
    //make sure it was was added
    assertEquals(4, map.getNumberOfGenes());
    assertEquals(4, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumGenes());
    assertEquals(3, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumConditions());
    assertEquals(0.47536945, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMinExpression(), 0.0);
    assertEquals(0.5418719, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMaxExpression(), 0.0);
}

Example 18 with EnrichmentMap

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

the class FileReaderTest method testExpression1ReaderEDBRnk.

@Test
public void testExpression1ReaderEDBRnk(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test expression file
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/ExpressionTestFile_edbrnk.rnk";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set gmt file name 
    params.getFiles().get(LegacySupport.DATASET1).setExpressionFileName(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);
    //make sure that the genes are empty
    assertEquals(0, map.getNumberOfGenes());
    //add the gene to the master list of genes
    map.addGene("GLS");
    map.addGene("PSMA1");
    map.addGene("ZP1");
    map.addGene("ZYX");
    //make sure all four genes have been associated
    assertEquals(4, map.getNumberOfGenes());
    //load expression file
    ExpressionFileReaderTask task = new ExpressionFileReaderTask(dataset);
    task.run(taskMonitor);
    //There was one more gene in the expression file that wasn't in the set of genes
    //make sure it was was added
    assertEquals(4, map.getNumberOfGenes());
    assertEquals(4, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumGenes());
    assertEquals(3, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumConditions());
    assertEquals(0.47536945, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMinExpression(), 0.0);
    assertEquals(0.5418719, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMaxExpression(), 0.0);
}

Example 19 with EnrichmentMap

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

the class FileReaderTest method testGSEAEnrichmentsReader.

//test GSEA enrichment results reader
@Test
public void testGSEAEnrichmentsReader(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/GSEA_enrichments1.xls";
    String testDataFileName2 = "src/test/resources/org/baderlab/csplugins/enrichmentmap/GSEA_enrichments2.xls";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set enrichment file name 
    params.getFiles().get(LegacySupport.DATASET1).setEnrichmentFileName1(testDataFileName);
    params.getFiles().get(LegacySupport.DATASET1).setEnrichmentFileName2(testDataFileName2);
    //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);
    ParseGSEAEnrichmentResults task = new ParseGSEAEnrichmentResults(dataset);
    task.run(taskMonitor);
    //Get the enrichment
    Map<String, EnrichmentResult> enrichments = map.getDataSet(LegacySupport.DATASET1).getEnrichments().getEnrichments();
    assertEquals(40, enrichments.size());
    //Check the contents of some of the genesets
    // example from file 1 (ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612)
    //check p-values
    assertEquals(0.0, ((GSEAResult) enrichments.get("ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612")).getPvalue(), 0.0);
    //check fdr value
    assertEquals(0.086938426, ((GSEAResult) enrichments.get("ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612")).getFdrqvalue(), 0.0);
    //check ES value
    assertEquals(0.6854155, ((GSEAResult) enrichments.get("ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612")).getES(), 0.0);
    //check NES
    assertEquals(2.1194055, ((GSEAResult) enrichments.get("ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612")).getNES(), 0.0);
    //check ranks at max
    assertEquals(836, ((GSEAResult) enrichments.get("ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612")).getRankAtMax());
    //check size
    assertEquals(27, ((GSEAResult) enrichments.get("ANTIGEN PROCESSING AND PRESENTATION%KEGG%HSA04612")).getGsSize());
    // example from file 2 (EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143)
    //check p-values
    assertEquals(0.040152963, ((GSEAResult) enrichments.get("EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143")).getPvalue(), 0.0);
    //check fdr value
    assertEquals(1.0, ((GSEAResult) enrichments.get("EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143")).getFdrqvalue(), 0.0);
    //check ES value
    assertEquals(-0.49066687, ((GSEAResult) enrichments.get("EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143")).getES(), 0.0);
    //check NES
    assertEquals(-1.477554, ((GSEAResult) enrichments.get("EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143")).getNES(), 0.0);
    //check ranks at max
    assertEquals(1597, ((GSEAResult) enrichments.get("EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143")).getRankAtMax());
    //check size
    assertEquals(17, ((GSEAResult) enrichments.get("EMBRYONIC HEART TUBE MORPHOGENESIS%GO%GO:0003143")).getGsSize());
}

Example 20 with EnrichmentMap

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

the class LegacySessionLoadTest method testSavingSession.

@Ignore
@SessionFile("em_session_2.2.cys")
public void testSavingSession() throws Exception {
    EnrichmentMapManager emManager = injector.getInstance(EnrichmentMapManager.class);
    Map<Long, EnrichmentMap> maps = emManager.getAllEnrichmentMaps();
    assertEquals(1, maps.size());
    SessionModelIO listener = injector.getInstance(SessionModelIO.class);
    listener.saveModel();
}