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

Example 11 with Method

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

the class FileReaderTest method testGMTFileReader.

@Test
public void testGMTFileReader(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/Genesetstestfile.gmt";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set gmt file name 
    params.getFiles().get(LegacySupport.DATASET1).setGMTFileName(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);
    //set up task
    GMTFileReaderTask task = new GMTFileReaderTask(dataset);
    task.run(taskMonitor);
    //test to make sure that the file loaded in 10 genesets with a total of 75 genes
    assertEquals(10, map.getAllGeneSets().size());
    assertEquals(75, map.getNumberOfGenes());
}

Example 12 with Method

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

the class FileReaderTest method testExpression1ReaderNormal.

@Test
public void testExpression1ReaderNormal(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test expression file
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/Expressiontestfile.gct";
    //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);
    //in order to load expression data the genes have to be registered with the application
    //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(59, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumConditions());
    assertEquals(0.008720342, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMinExpression(), 0.0);
    assertEquals(5.131481026, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMaxExpression(), 0.0);
}

Example 13 with Method

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

the class FileReaderTest method testBingoEnrichmentsReader.

//test Bingo enrichment results
@Test
public void testBingoEnrichmentsReader(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test enrichment files - Bingo
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/BingoResults.bgo";
    //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);
    ParseBingoEnrichmentResults task = new ParseBingoEnrichmentResults(dataset);
    task.run(taskMonitor);
    //Get the enrichment
    Map<String, EnrichmentResult> enrichments = map.getDataSet(LegacySupport.DATASET1).getEnrichments().getEnrichments();
    assertEquals(74, enrichments.size());
    //check p-values
    assertEquals(0.0010354, ((GenericResult) enrichments.get("NUCLEOLAR PART")).getPvalue(), 0.0);
    //check fdr value
    assertEquals(0.047796, ((GenericResult) enrichments.get("NUCLEOLAR PART")).getFdrqvalue(), 0.0);
    //check geneset siz
    assertEquals(5, ((GenericResult) enrichments.get("NUCLEOLAR PART")).getGsSize());
    //check p-values
    assertEquals(0.0000000000016209, ((GenericResult) enrichments.get("NUCLEOLUS")).getPvalue(), 0.0);
    //check fdr value
    assertEquals(0.0000000042203, ((GenericResult) enrichments.get("NUCLEOLUS")).getFdrqvalue(), 0.0);
    //check geneset siz
    assertEquals(43, ((GenericResult) enrichments.get("NUCLEOLUS")).getGsSize());
}

Example 14 with Method

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

the class FileReaderTest method testExpression1ReaderCommentLines.

@Test
public void testExpression1ReaderCommentLines(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load the test expression file
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/Expressiontestfile_comments.gct";
    //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(5.131481026, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMaxExpression(), 0.0);
    assertEquals(4, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumGenes());
    assertEquals(59, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getNumConditions());
    assertEquals(0.008720342, map.getDataSet(LegacySupport.DATASET1).getExpressionSets().getMinExpression(), 0.0);
}

Example 15 with Method

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

the class GeneSetSimilarityTest method before.

@Before
public void before(Provider<EnrichmentMapParameters> empFactory) throws Exception {
    //load Genesets from the gmt file associated with this test
    String testDataFileName = "src/test/resources/org/baderlab/csplugins/enrichmentmap/model/Genesetstestfile.gmt";
    //create a new instance of the parameters
    EnrichmentMapParameters params = empFactory.get();
    //set gmt file name 
    params.getFiles().get(LegacySupport.DATASET1).setGMTFileName(testDataFileName);
    //Create a new Enrichment map
    map = new EnrichmentMap(params.getCreationParameters(), serviceRegistrar);
    Method method = EnrichmentMapParameters.stringToMethod(params.getMethod());
    DataSetFiles files = params.getFiles().get(LegacySupport.DATASET1);
    dataset = map.createDataSet(LegacySupport.DATASET1, method, files);
    //set up task
    GMTFileReaderTask task = new GMTFileReaderTask(dataset);
    task.run(taskMonitor);
    this.dataset.setGeneSetsOfInterest(this.dataset.getSetOfGeneSets());
}