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

Example 1 with BioAssayDimensionValueObject

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

the class ExperimentalDesignVisualizationServiceImpl method prepare.

/**
 * Gets the bioassay dimensions for the experiments associated with the given vectors. These are cached for later
 * re-use.
 */
private void prepare(Collection<DoubleVectorValueObject> dvvOs) {
    if (dvvOs == null)
        return;
    for (DoubleVectorValueObject vec : dvvOs) {
        if (vec == null) {
            log.debug("DoubleVectorValueObject is null");
            continue;
        }
        if (vec.isReorganized()) {
            // wouldn't normally be the case...
            continue;
        }
        ExpressionExperimentValueObject ee = vec.getExpressionExperiment();
        /*
             * Problem: we can't have two layouts for one experiment, which is actually required if there is more than
             * one bioassay dimension. However, this rarely matters. See bug 3775
             */
        if (cachedLayouts.containsKey(ee.getId())) {
            continue;
        } else if (vec.getClass().isInstance(ExpressionExperimentSubsetValueObject.class)) {
            ExpressionExperimentSubsetValueObject eesvo = (ExpressionExperimentSubsetValueObject) vec.getExpressionExperiment();
            if (eesvo.getSourceExperiment() != null && cachedLayouts.containsKey(eesvo.getSourceExperiment())) {
                continue;
            }
        }
        BioAssayDimensionValueObject bioAssayDimension = this.getBioAssayDimensionForVector(vec);
        ExpressionExperiment actualEe = this.getExperimentForVector(vec, ee);
        assert bioAssayDimension != null;
        LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> experimentalDesignLayout = this.getExperimentalDesignLayout(actualEe, expressionExperimentService.getBioAssayDimensions(actualEe));
        cachedLayouts.put(ee.getId(), experimentalDesignLayout);
    }
}

Example 2 with BioAssayDimensionValueObject

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

the class ExperimentalDesignVisualizationServiceImpl method getExperimentalDesignLayout.

/**
 * @param bds a BioAssayDimension that represents the BioAssayDimensionValueObject. This is only needed to avoid
 *            making ExpressionMatrix use value objects, otherwise we could use the BioAssayDimensionValueObject
 * @return A "Layout": a map of bioassays to map of factors to doubles that represent the position in the layout.
 */
private LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> getExperimentalDesignLayout(ExpressionExperiment experiment, Collection<BioAssayDimension> bds) {
    LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> result = new LinkedHashMap<>();
    ExpressionDataMatrix<Object> mat = new EmptyExpressionMatrix(bds);
    // This is the place the actual sort order is determined.
    List<BioMaterial> bms = ExpressionDataMatrixColumnSort.orderByExperimentalDesign(mat);
    Map<Long, Double> fvV = new HashMap<>();
    assert experiment != null;
    assert experiment.getExperimentalDesign() != null;
    if (experiment.getExperimentalDesign().getExperimentalFactors().isEmpty()) {
        // Case of no experimental design; just put in a dummy factor.
        ExperimentalFactor dummyFactor = ExperimentalFactor.Factory.newInstance();
        dummyFactor.setName("No factors");
        for (BioMaterial bm : bms) {
            int j = mat.getColumnIndex(bm);
            Collection<BioAssay> bas = mat.getBioAssaysForColumn(j);
            for (BioAssay ba : bas) {
                BioAssayValueObject baVo = new BioAssayValueObject(ba, false);
                result.put(baVo, new LinkedHashMap<ExperimentalFactor, Double>());
                result.get(baVo).put(dummyFactor, 0.0);
            }
        }
        return result;
    }
    assert !experiment.getExperimentalDesign().getExperimentalFactors().isEmpty();
    // Map<ExperimentalFactor, Map<FactorValue, Double>> continuousRanges = new HashMap<>();
    for (ExperimentalFactor ef : experiment.getExperimentalDesign().getExperimentalFactors()) {
        if (ef.getFactorValues().isEmpty()) {
            // this can happen if the design isn't complete.
            continue;
        }
        for (FactorValue fv : ef.getFactorValues()) {
            assert fv.getId() != null;
            // the id is just used as a convenience.
            fvV.put(fv.getId(), new Double(fv.getId()));
        }
    }
    assert !fvV.isEmpty();
    assert !bms.isEmpty();
    // either bioassay dimension.
    for (BioMaterial bm : bms) {
        int j = mat.getColumnIndex(bm);
        Collection<BioAssay> bas = mat.getBioAssaysForColumn(j);
        Collection<FactorValue> fvs = bm.getFactorValues();
        for (BioAssay ba : bas) {
            BioAssayValueObject baVo = new BioAssayValueObject(ba, false);
            result.put(baVo, new LinkedHashMap<ExperimentalFactor, Double>(fvs.size()));
            for (FactorValue fv : fvs) {
                assert fv.getId() != null;
                assert fvV.containsKey(fv.getId());
                ExperimentalFactor ef = fv.getExperimentalFactor();
                Double value;
                if (fv.getMeasurement() != null) {
                    try {
                        value = Double.parseDouble(fv.getMeasurement().getValue());
                    } catch (NumberFormatException e) {
                        // not good.
                        value = fvV.get(fv.getId());
                    }
                } else {
                    value = fvV.get(fv.getId());
                }
                assert result.containsKey(baVo);
                assert value != null;
                result.get(baVo).put(ef, value);
            }
        }
    }
    return result;
}

Example 3 with BioAssayDimensionValueObject

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

the class ExperimentalDesignVisualizationServiceImpl method extendLayout.

/**
 * See bug 3775. For experiments which have more than one bioassay dimension, we typically have to "extend" the
 * layout to include more bioassays. Because the ordering is defined by the factor values associated with the
 * underlying biomaterials, this is going to be okay.
 */
private LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> extendLayout(DoubleVectorValueObject vec, Long eeId) {
    BioAssayDimensionValueObject bioAssayDimension = this.getBioAssayDimensionForVector(vec);
    ExpressionExperimentValueObject ee = vec.getExpressionExperiment();
    ExpressionExperiment actualEe = this.getExperimentForVector(vec, ee);
    LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> extension = this.getExperimentalDesignLayout(actualEe, expressionExperimentService.getBioAssayDimensions(actualEe));
    for (BioAssayValueObject vbaVo : bioAssayDimension.getBioAssays()) {
        assert extension.containsKey(vbaVo);
    }
    for (BioAssayValueObject vbaVo : vec.getBioAssays()) {
        assert extension.containsKey(vbaVo);
    }
    cachedLayouts.get(eeId).putAll(extension);
    return cachedLayouts.get(eeId);
}