Examples with ExperimentExpressionLevelsValueObject ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject used on opensource projects

Example 1 with ExperimentExpressionLevelsValueObject

use of ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorServiceImpl method addExperimentGeneVectors.

/**
 * Creates an ExperimentExpressionLevelValueObject for the given experiment and collection of double vector VOs, and
 * adds it to the given vos collection.
 *
 * @param vos     the collection to add the result to.
 * @param ee      the experiment the vectors belong to.
 * @param vectors the vectors to create the new ExperimentExpressionLevelsVO with.
 */
private void addExperimentGeneVectors(Collection<ExperimentExpressionLevelsValueObject> vos, ExpressionExperiment ee, Collection<DoubleVectorValueObject> vectors, boolean keepGeneNonSpecific, String consolidateMode) {
    Map<Gene, List<DoubleVectorValueObject>> vectorsPerGene = new HashMap<>();
    if (vectors == null) {
        return;
    }
    for (DoubleVectorValueObject v : vectors) {
        if (!v.getExpressionExperiment().getId().equals(ee.getId())) {
            continue;
        }
        if (v.getGenes() == null || v.getGenes().isEmpty()) {
            if (!vectorsPerGene.containsKey(null)) {
                vectorsPerGene.put(null, new LinkedList<DoubleVectorValueObject>());
            }
            vectorsPerGene.get(null).add(v);
        }
        for (Long gId : v.getGenes()) {
            Gene g = geneService.load(gId);
            if (g != null) {
                if (!vectorsPerGene.containsKey(g)) {
                    vectorsPerGene.put(g, new LinkedList<DoubleVectorValueObject>());
                }
                vectorsPerGene.get(g).add(v);
            }
        }
    }
    vos.add(new ExperimentExpressionLevelsValueObject(ee.getId(), vectorsPerGene, keepGeneNonSpecific, consolidateMode));
}

Example 2 with ExperimentExpressionLevelsValueObject

use of ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorServiceImpl method getExpressionLevels.

@Override
@Transactional(readOnly = true)
public Collection<ExperimentExpressionLevelsValueObject> getExpressionLevels(Collection<ExpressionExperiment> ees, Collection<Gene> genes, boolean keepGeneNonSpecific, String consolidateMode) {
    Collection<DoubleVectorValueObject> vectors = this.getProcessedDataArrays(ees, EntityUtils.getIds(genes));
    Collection<ExperimentExpressionLevelsValueObject> vos = new ArrayList<>(ees.size());
    // Adapted from DEDV controller
    for (ExpressionExperiment ee : ees) {
        Map<Gene, List<DoubleVectorValueObject>> vectorsPerGene = new HashMap<>();
        for (DoubleVectorValueObject v : vectors) {
            if (!v.getExpressionExperiment().getId().equals(ee.getId())) {
                continue;
            }
            if (v.getGenes() == null || v.getGenes().isEmpty()) {
                continue;
            }
            for (Gene g : genes) {
                if (v.getGenes().contains(g.getId())) {
                    if (!vectorsPerGene.containsKey(g)) {
                        vectorsPerGene.put(g, new LinkedList<DoubleVectorValueObject>());
                    }
                    vectorsPerGene.get(g).add(v);
                }
            }
        }
        vos.add(new ExperimentExpressionLevelsValueObject(ee.getId(), vectorsPerGene, keepGeneNonSpecific, consolidateMode));
    }
    return vos;
}

Example 3 with ExperimentExpressionLevelsValueObject

use of ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorServiceImpl method getExpressionLevelsDiffEx.

@Override
@Transactional(readOnly = true)
public Collection<ExperimentExpressionLevelsValueObject> getExpressionLevelsDiffEx(Collection<ExpressionExperiment> ees, Long diffExResultSetId, double threshold, int max, boolean keepGeneNonSpecific, String consolidateMode) {
    Collection<ExperimentExpressionLevelsValueObject> vos = new ArrayList<>();
    // Adapted from DEDV controller
    for (ExpressionExperiment ee : ees) {
        Collection<DoubleVectorValueObject> vectors = this.getDiffExVectors(diffExResultSetId, threshold, max);
        this.addExperimentGeneVectors(vos, ee, vectors, keepGeneNonSpecific, consolidateMode);
    }
    return vos;
}

Example 4 with ExperimentExpressionLevelsValueObject

use of ubic.gemma.model.expression.bioAssayData.ExperimentExpressionLevelsValueObject in project Gemma by PavlidisLab.

the class ProcessedExpressionDataVectorServiceImpl method getExpressionLevelsPca.

@Override
@Transactional(readOnly = true)
public Collection<ExperimentExpressionLevelsValueObject> getExpressionLevelsPca(Collection<ExpressionExperiment> ees, int limit, int component, boolean keepGeneNonSpecific, String consolidateMode) {
    Collection<ExperimentExpressionLevelsValueObject> vos = new ArrayList<>(ees.size());
    // Adapted from DEDV controller
    for (ExpressionExperiment ee : ees) {
        Collection<DoubleVectorValueObject> vectors = svdService.getTopLoadedVectors(ee.getId(), component, limit).values();
        this.addExperimentGeneVectors(vos, ee, vectors, keepGeneNonSpecific, consolidateMode);
    }
    return vos;
}