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

Example 1 with DiscreteTaskMonitor

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

the class CreateDiseaseSignatureTaskParallel method startBuildDiseaseSignatureParallel.

/**
	 * Returns immediately, need to wait on the executor to join all threads.
	 */
private Map<SimilarityKey, GenesetSimilarity> startBuildDiseaseSignatureParallel(TaskMonitor tm, ExecutorService executor, Set<String> enrichmentGeneSetNames, Map<String, GeneSet> signatureGeneSets) {
    DiscreteTaskMonitor taskMonitor = discreteTaskMonitor(tm, signatureGeneSets.size());
    // Gene universe is all enrichment genes in the map
    Set<Integer> geneUniverse = map.getAllEnrichmentGenes();
    Map<SimilarityKey, GenesetSimilarity> geneSetSimilarities = new ConcurrentHashMap<>();
    for (String hubName : signatureGeneSets.keySet()) {
        GeneSet sigGeneSet = signatureGeneSets.get(hubName);
        Set<Integer> sigGenesInUniverse = Sets.intersection(sigGeneSet.getGenes(), geneUniverse);
        // Compute similarities in batches
        executor.execute(() -> {
            loop: for (String geneSetName : enrichmentGeneSetNames) {
                for (EMDataSet dataSet : dataSets) {
                    if (Thread.interrupted())
                        break loop;
                    GeneSet enrGeneSet = dataSet.getSetOfGeneSets().getGeneSetByName(geneSetName);
                    if (enrGeneSet != null) {
                        // restrict to a common gene universe
                        Set<Integer> enrGenes = Sets.intersection(enrGeneSet.getGenes(), geneUniverse);
                        Set<Integer> union = Sets.union(sigGeneSet.getGenes(), enrGenes);
                        Set<Integer> intersection = Sets.intersection(sigGenesInUniverse, enrGenes);
                        if (!intersection.isEmpty()) {
                            double coeffecient = ComputeSimilarityTaskParallel.computeSimilarityCoeffecient(map.getParams(), intersection, union, sigGeneSet.getGenes(), enrGenes);
                            GenesetSimilarity comparison = new GenesetSimilarity(hubName, geneSetName, coeffecient, INTERACTION, intersection);
                            PostAnalysisFilterType filterType = params.getRankTestParameters().getType();
                            switch(filterType) {
                                case HYPERGEOM:
                                    int hyperUniverseSize1 = getHypergeometricUniverseSize(dataSet);
                                    hypergeometric(hyperUniverseSize1, sigGenesInUniverse, enrGenes, intersection, comparison);
                                    break;
                                case MANN_WHIT_TWO_SIDED:
                                case MANN_WHIT_GREATER:
                                case MANN_WHIT_LESS:
                                    mannWhitney(intersection, comparison, dataSet);
                                default:
                                    // want mann-whit to fall through
                                    // #70 calculate hypergeometric also
                                    int hyperUniverseSize2 = map.getNumberOfGenes();
                                    hypergeometric(hyperUniverseSize2, sigGenesInUniverse, enrGenes, intersection, comparison);
                                    break;
                            }
                            SimilarityKey key = new SimilarityKey(hubName, geneSetName, INTERACTION, dataSet.getName());
                            geneSetSimilarities.put(key, comparison);
                        }
                    }
                }
            }
            taskMonitor.inc();
        });
    }
    return geneSetSimilarities;
}

Example 2 with DiscreteTaskMonitor

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

the class CreateDiseaseSignatureTaskParallel method discreteTaskMonitor.

private static DiscreteTaskMonitor discreteTaskMonitor(TaskMonitor tm, int size) {
    DiscreteTaskMonitor taskMonitor = new DiscreteTaskMonitor(tm, size);
    taskMonitor.setTitle("Post Analysis Geneset Similarities...");
    taskMonitor.setStatusMessageTemplate("Computing Geneset Similarity: {0} of {1} tasks");
    return taskMonitor;
}

Example 3 with DiscreteTaskMonitor

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

the class InitializeGenesetsOfInterestTask method initializeSets.

/**
	 * filter the genesets, restricting them to only those passing the user
	 * specified thresholds.
	 * 
	 * @return true if successful and false otherwise.
	 */
public boolean initializeSets(TaskMonitor tm) {
    if (tm == null)
        tm = new NullTaskMonitor();
    DiscreteTaskMonitor taskMonitor = new DiscreteTaskMonitor(tm, map.getDataSetCount());
    //create subset of genesets that contains only the genesets of interest with pvalue and qbalue less than values specified by the user.
    //Go through each Dataset populating the Gene set of interest in each dataset object
    Map<String, EMDataSet> datasets = map.getDataSets();
    // count how many experiments (DataSets) contain the geneset
    Optional<Integer> minExperiments = map.getParams().getMinExperiments();
    Map<String, Integer> occurrences = minExperiments.isPresent() ? new HashMap<>() : null;
    for (String datasetName : datasets.keySet()) {
        taskMonitor.inc();
        EMDataSet dataset = datasets.get(datasetName);
        // all these maps use the geneset name as key
        Map<String, EnrichmentResult> enrichmentResults = dataset.getEnrichments().getEnrichments();
        Map<String, GeneSet> genesets = dataset.getSetOfGeneSets().getGeneSets();
        Map<String, GeneSet> genesetsOfInterest = dataset.getGeneSetsOfInterest().getGeneSets();
        // If there are no genesets associated with this dataset then get the complete set assumption being that the gmt file applies to all datasets.
        if (genesets == null || genesets.isEmpty()) {
            genesets = map.getAllGeneSets();
        }
        //if there are no enrichment Results then do nothing
        if (enrichmentResults == null || enrichmentResults.isEmpty()) {
            return false;
        }
        //iterate through the GSEA Results to figure out which genesets we want to use
        for (String genesetName : enrichmentResults.keySet()) {
            EnrichmentResult result = enrichmentResults.get(genesetName);
            // update rank at max for leading edge calculation
            if (dataset.getMethod() == Method.GSEA) {
                Ranking ranks = dataset.getExpressionSets().getRanksByName(datasetName);
                updateRankAtMax((GSEAResult) result, ranks);
            }
            if (result.geneSetOfInterest(map.getParams())) {
                GeneSet geneset = genesets.get(genesetName);
                if (geneset != null) {
                    // while we are checking, update the size of the genesets based on post filtered data
                    result.setGsSize(geneset.getGenes().size());
                    if (occurrences != null) {
                        occurrences.merge(genesetName, 1, (v, d) -> v + 1);
                    }
                    genesetsOfInterest.put(genesetName, geneset);
                } else if (throwIfMissing) {
                    throw new IllegalThreadStateException("The Geneset: " + genesetName + " is not found in the GMT file.");
                }
            }
        }
    }
    // Remove gene-sets that don't pass the minimum occurrence cutoff
    if (occurrences != null) {
        for (EMDataSet dataset : datasets.values()) {
            Map<String, GeneSet> genesetsOfInterest = dataset.getGeneSetsOfInterest().getGeneSets();
            genesetsOfInterest.keySet().removeIf(geneset -> occurrences.getOrDefault(geneset, 0) < minExperiments.get());
        }
    }
    return true;
}

Example 4 with DiscreteTaskMonitor

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

the class ComputeSimilarityTaskParallel method discreteTaskMonitor.

private static DiscreteTaskMonitor discreteTaskMonitor(TaskMonitor tm, int size) {
    DiscreteTaskMonitor taskMonitor = new DiscreteTaskMonitor(tm, size);
    taskMonitor.setTitle("Computing Geneset Similarities...");
    taskMonitor.setStatusMessageTemplate("Computing Geneset Similarity: {0} of {1} tasks");
    return taskMonitor;
}

Example 5 with DiscreteTaskMonitor

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

the class CreateDiseaseSignatureNetworkTask method run.

/**
	 * This task is NOT cancellable.
	 */
@Override
public void run(TaskMonitor tm) {
    tm.setTitle("Post Analysis Geneset Similarities...");
    CyNetwork network = networkManager.getNetwork(map.getNetworkID());
    CyNetworkView networkView = getNetworKView(network);
    taskResult.setNetwork(network);
    taskResult.setNetworkView(networkView);
    // Gene universe is all enrichment genes in the map
    Set<Integer> geneUniverse = map.getAllEnrichmentGenes();
    String prefix = params.getAttributePrefix();
    //get the node attribute and edge attribute tables
    tm.setStatusMessage("Creating Columns");
    CyTable edgeTable = createEdgeColumns(network, "", prefix);
    CyTable nodeTable = createNodeColumns(network, "", prefix);
    tm.setProgress(0.1);
    tm.setStatusMessage("Caching Nodes");
    existingEdgeCache = createExistingEdgeCache(prefix, network, edgeTable);
    tm.setProgress(0.2);
    EMSignatureDataSet sigDataSet = createSignatureDataSet();
    // Create Signature Hub Nodes
    tm.setStatusMessage("Creating Nodes");
    signatureGeneSets.forEach(sigDataSet.getGeneSetsOfInterest()::addGeneSet);
    signatureGeneSets.forEach((hubName, sigGeneSet) -> createHubNode(hubName, network, networkView, prefix, edgeTable, nodeTable, geneUniverse, sigGeneSet, sigDataSet));
    tm.setProgress(0.3);
    // Layout nodes
    tm.setStatusMessage("Laying out Nodes");
    layoutHubNodes(networkView);
    tm.setProgress(0.4);
    // Create Signature Hub Edges
    tm.setStatusMessage("Creating Edges");
    DiscreteTaskMonitor dtm = new DiscreteTaskMonitor(tm, geneSetSimilarities.size(), 0.4, 0.9);
    dtm.setStatusMessageTemplate("Similarity {0} of {1}");
    for (SimilarityKey similarityKey : geneSetSimilarities.keySet()) {
        boolean passedCutoff = passesCutoff(similarityKey, sigDataSet);
        createEdge(similarityKey, network, networkView, prefix, edgeTable, nodeTable, passedCutoff, sigDataSet);
        dtm.inc();
    }
    // Set edge widths
    tm.setStatusMessage("Setting Edge Widths");
    widthFunctionProvider.get().setEdgeWidths(network, prefix, tm);
    tm.setProgress(1.0);
    // Add the new data set to the map
    map.addSignatureDataSet(sigDataSet);
}