Examples with CreateEnrichmentMapTaskFactory org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory used on opensource projects

Example 1 with CreateEnrichmentMapTaskFactory

use of org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory in project EnrichmentMapApp by BaderLab.

the class EMBuildCommandTask method buildEnrichmentMap.

/**
	 * buildEnrichmentMap - parses all GSEA input files and creates an enrichment map
	 */
public void buildEnrichmentMap() {
    // Note we must continue to use the old constants from EnrichmentMapParameters for backwards compatibility
    Method method = EnrichmentMapParameters.stringToMethod(analysisType.getSelectedValue());
    SimilarityMetric metric = EnrichmentMapParameters.stringToSimilarityMetric(coeffecients.getSelectedValue());
    //Set Dataset1 Files
    DataSetFiles dataset1files = new DataSetFiles();
    if (gmtFile != null)
        dataset1files.setGMTFileName(gmtFile.getAbsolutePath());
    if (expressionDataset1 != null)
        dataset1files.setExpressionFileName(expressionDataset1.getAbsolutePath());
    if (enrichmentsDataset1 != null)
        dataset1files.setEnrichmentFileName1(enrichmentsDataset1.getAbsolutePath());
    if (enrichments2Dataset1 != null)
        dataset1files.setEnrichmentFileName2(enrichments2Dataset1.getAbsolutePath());
    if (ranksDataset1 != null)
        dataset1files.setRankedFile(ranksDataset1.getAbsolutePath());
    if (classDataset1 != null)
        dataset1files.setClassFile(classDataset1.getAbsolutePath());
    if (phenotype1Dataset1 != null)
        dataset1files.setPhenotype1(phenotype1Dataset1);
    if (phenotype2Dataset1 != null)
        dataset1files.setPhenotype2(phenotype2Dataset1);
    //Set Dataset2 Files
    DataSetFiles dataset2files = new DataSetFiles();
    if (expressionDataset2 != null)
        dataset2files.setExpressionFileName(expressionDataset2.getAbsolutePath());
    if (enrichmentsDataset2 != null)
        dataset2files.setEnrichmentFileName1(enrichmentsDataset2.getAbsolutePath());
    if (enrichments2Dataset2 != null)
        dataset2files.setEnrichmentFileName2(enrichments2Dataset2.getAbsolutePath());
    if (ranksDataset2 != null)
        dataset2files.setRankedFile(ranksDataset2.getAbsolutePath());
    if (classDataset2 != null)
        dataset2files.setClassFile(classDataset2.getAbsolutePath());
    if (phenotype1Dataset2 != null)
        dataset2files.setPhenotype1(phenotype1Dataset2);
    if (phenotype2Dataset2 != null)
        dataset2files.setPhenotype2(phenotype2Dataset2);
    List<DataSetParameters> dataSets = new ArrayList<>(2);
    dataSets.add(new DataSetParameters(LegacySupport.DATASET1, method, dataset1files));
    if (!dataset2files.isEmpty()) {
        dataSets.add(new DataSetParameters(LegacySupport.DATASET2, method, dataset2files));
    }
    String prefix = legacySupport.getNextAttributePrefix();
    EMCreationParameters creationParams = new EMCreationParameters(prefix, pvalue, qvalue, NESFilter.ALL, Optional.empty(), metric, similaritycutoff, propertyManager.getDefaultCombinedConstant());
    if (distinctEdges != null)
        creationParams.setCreateDistinctEdges(distinctEdges);
    else if (!dataset2files.isEmpty())
        creationParams.setCreateDistinctEdges(true);
    CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(creationParams, dataSets);
    insertTasksAfterCurrentTask(taskFactory.createTaskIterator());
}

Example 2 with CreateEnrichmentMapTaskFactory

use of org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory in project EnrichmentMapApp by BaderLab.

the class CreateEnrichmentMapTaskTest method buildEnrichmentMap.

protected void buildEnrichmentMap(EMCreationParameters params, DataSetFiles datasetFiles, String datasetName) {
    List<DataSetParameters> dataSets = Arrays.asList(new DataSetParameters(datasetName, Method.Generic, datasetFiles));
    CreateEnrichmentMapTaskFactory.Factory masterMapTaskFactoryFactory = injector.getInstance(CreateEnrichmentMapTaskFactory.Factory.class);
    CreateEnrichmentMapTaskFactory taskFactory = masterMapTaskFactoryFactory.create(params, dataSets);
    TaskIterator taskIterator = taskFactory.createTaskIterator();
    SerialTestTaskManager taskManager = new SerialTestTaskManager();
    taskManager.execute(taskIterator);
}

Example 3 with CreateEnrichmentMapTaskFactory

use of org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory in project EnrichmentMapApp by BaderLab.

the class MasterDetailDialogPage method finish.

@Override
public void finish() {
    if (!validateInput())
        return;
    String prefix = legacySupport.getNextAttributePrefix();
    SimilarityMetric similarityMetric = cutoffPanel.getSimilarityMetric();
    double pvalue = cutoffPanel.getPValue();
    double qvalue = cutoffPanel.getQValue();
    NESFilter nesFilter = cutoffPanel.getNESFilter();
    double cutoff = cutoffPanel.getCutoff();
    double combined = cutoffPanel.getCombinedConstant();
    Optional<Integer> minExperiments = cutoffPanel.getMinimumExperiments();
    EMCreationParameters params = new EMCreationParameters(prefix, pvalue, qvalue, nesFilter, minExperiments, similarityMetric, cutoff, combined);
    params.setCreateDistinctEdges(distinctEdgesCheckbox.isSelected());
    List<DataSetParameters> dataSets = dataSetListModel.toList().stream().map(DataSetListItem::getDetailPanel).map(DetailPanel::createDataSetParameters).filter(x -> x != null).collect(Collectors.toList());
    // Overwrite all the expression files if the common file has been provided
    String exprPath = commonPanel.getExpressionFile();
    if (!isNullOrEmpty(exprPath)) {
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setExpressionFileName(exprPath);
        }
    }
    // Overwrite all the gmt files if a common file has been provided
    String gmtPath = commonPanel.getGmtFile();
    if (!isNullOrEmpty(gmtPath)) {
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setGMTFileName(gmtPath);
        }
    }
    CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
    TaskIterator tasks = taskFactory.createTaskIterator();
    // Close this dialog after the progress dialog finishes normally
    tasks.append(new AbstractTask() {

        public void run(TaskMonitor taskMonitor) {
            callback.close();
        }
    });
    dialogTaskManager.execute(tasks);
}

Example 4 with CreateEnrichmentMapTaskFactory

use of org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory in project EnrichmentMapApp by BaderLab.

the class EMGseaCommandTask method buildEnrichmentMap.

private void buildEnrichmentMap() {
    //set all files as extracted from the edb directory
    List<DataSetParameters> dataSets = new ArrayList<>(2);
    DataSetFiles files1 = initializeFiles(edbdir, expressionfile);
    dataSets.add(new DataSetParameters(LegacySupport.DATASET1, Method.GSEA, files1));
    //only add second dataset if there is a second edb directory.
    if (edbdir2 != null && !edbdir2.equalsIgnoreCase("")) {
        DataSetFiles files2 = initializeFiles(edbdir2, expressionfile2);
        dataSets.add(new DataSetParameters(LegacySupport.DATASET2, Method.GSEA, files2));
    }
    SimilarityMetric metric = EnrichmentMapParameters.stringToSimilarityMetric(similaritymetric.getSelectedValue());
    String prefix = legacySupport.getNextAttributePrefix();
    EMCreationParameters creationParams = new EMCreationParameters(prefix, pvalue, qvalue, NESFilter.ALL, Optional.empty(), metric, overlap, combinedconstant);
    CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(creationParams, dataSets);
    insertTasksAfterCurrentTask(taskFactory.createTaskIterator());
}

Example 5 with CreateEnrichmentMapTaskFactory

use of org.baderlab.csplugins.enrichmentmap.task.CreateEnrichmentMapTaskFactory in project EnrichmentMapApp by BaderLab.

the class ResolverCommandTask method run.

@Override
public void run(TaskMonitor taskMonitor) throws Exception {
    logger.info("Running EnrichmentMap Data Set Resolver Task");
    // Scan root folder (note: throws exception if no data sets were found)
    ResolverTask resolverTask = new ResolverTask(rootFolder);
    // blocks
    taskManager.execute(new TaskIterator(resolverTask));
    List<DataSetParameters> dataSets = resolverTask.getDataSetResults();
    logger.info("resolved " + dataSets.size() + " data sets");
    dataSets.forEach(params -> logger.info(params.toString()));
    // Overwrite all the expression files if the common file has been provided
    if (commonExpressionFile != null) {
        if (!commonExpressionFile.canRead()) {
            throw new IllegalArgumentException("Cannot read commonExpressionFile: " + commonExpressionFile);
        }
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setExpressionFileName(commonExpressionFile.getAbsolutePath());
        }
    }
    // Overwrite all the gmt files if a common file has been provided
    if (commonGMTFile != null) {
        if (!commonGMTFile.canRead()) {
            throw new IllegalArgumentException("Cannot read commonGMTFile: " + commonGMTFile);
        }
        for (DataSetParameters dsp : dataSets) {
            dsp.getFiles().setGMTFileName(commonGMTFile.getAbsolutePath());
        }
    }
    // Create Enrichment Map
    String prefix = legacySupport.getNextAttributePrefix();
    SimilarityMetric sm = SimilarityMetric.valueOf(similarityMetric.getSelectedValue());
    NESFilter nesf = NESFilter.valueOf(nesFilter.getSelectedValue());
    String info = String.format("prefix:%s, pvalue:%f, qvalue:%f, nesFilter:%s, minExperiments:%d, similarityMetric:%s, similarityCutoff:%f, combinedConstant:%f", prefix, pvalue, qvalue, nesf, minExperiments, sm, similarityCutoff, combinedConstant);
    logger.info(info);
    EMCreationParameters params = new EMCreationParameters(prefix, pvalue, qvalue, nesf, Optional.ofNullable(minExperiments), sm, similarityCutoff, combinedConstant);
    params.setCreateDistinctEdges(distinctEdges);
    CreateEnrichmentMapTaskFactory taskFactory = taskFactoryFactory.create(params, dataSets);
    TaskIterator tasks = taskFactory.createTaskIterator();
    taskManager.execute(tasks);
    logger.info("Done.");
}