Examples with DenseDoubleMatrix ubic.basecode.dataStructure.matrix.DenseDoubleMatrix used on opensource projects

Example 1 with DenseDoubleMatrix

use of ubic.basecode.dataStructure.matrix.DenseDoubleMatrix in project Gemma by PavlidisLab.

the class DataUpdaterTest method testAddData.

@Test
public void testAddData() throws Exception {
    /*
         * Load a regular data set that has no data. Platform is (basically) irrelevant.
         */
    geoService.setGeoDomainObjectGenerator(new GeoDomainObjectGeneratorLocal(this.getTestFileBasePath()));
    ExpressionExperiment ee;
    try {
        // RNA-seq data.
        Collection<?> results = geoService.fetchAndLoad("GSE37646", false, true, false);
        ee = (ExpressionExperiment) results.iterator().next();
    } catch (AlreadyExistsInSystemException e) {
        // log.warn( "Test skipped because GSE37646 was not removed from the system prior to test" );
        ee = (ExpressionExperiment) ((List<?>) e.getData()).get(0);
    }
    ee = experimentService.thawLite(ee);
    List<BioAssay> bioAssays = new ArrayList<>(ee.getBioAssays());
    assertEquals(31, bioAssays.size());
    List<BioMaterial> bms = new ArrayList<>();
    for (BioAssay ba : bioAssays) {
        bms.add(ba.getSampleUsed());
    }
    targetArrayDesign = this.getTestPersistentArrayDesign(100, true);
    DoubleMatrix<CompositeSequence, BioMaterial> rawMatrix = new DenseDoubleMatrix<>(targetArrayDesign.getCompositeSequences().size(), bms.size());
    /*
         * make up some fake data on another platform, and match it to those samples
         */
    for (int i = 0; i < rawMatrix.rows(); i++) {
        for (int j = 0; j < rawMatrix.columns(); j++) {
            rawMatrix.set(i, j, (i + 1) * (j + 1) * Math.random() / 100.0);
        }
    }
    List<CompositeSequence> probes = new ArrayList<>(targetArrayDesign.getCompositeSequences());
    rawMatrix.setRowNames(probes);
    rawMatrix.setColumnNames(bms);
    QuantitationType qt = this.makeQt(true);
    ExpressionDataDoubleMatrix data = new ExpressionDataDoubleMatrix(ee, qt, rawMatrix);
    assertNotNull(data.getBestBioAssayDimension());
    assertEquals(rawMatrix.columns(), data.getBestBioAssayDimension().getBioAssays().size());
    assertEquals(probes.size(), data.getMatrix().rows());
    /*
         * Replace it.
         */
    ee = dataUpdater.replaceData(ee, targetArrayDesign, data);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    ee = experimentService.thaw(ee);
    for (BioAssay ba : ee.getBioAssays()) {
        assertEquals(targetArrayDesign, ba.getArrayDesignUsed());
    }
    assertEquals(100, ee.getRawExpressionDataVectors().size());
    for (RawExpressionDataVector v : ee.getRawExpressionDataVectors()) {
        assertTrue(v.getQuantitationType().getIsPreferred());
    }
    assertEquals(100, ee.getProcessedExpressionDataVectors().size());
    Collection<DoubleVectorValueObject> processedDataArrays = dataVectorService.getProcessedDataArrays(ee);
    for (DoubleVectorValueObject v : processedDataArrays) {
        assertEquals(31, v.getBioAssays().size());
    }
    /*
         * Test adding data (non-preferred)
         */
    qt = this.makeQt(false);
    ExpressionDataDoubleMatrix moreData = new ExpressionDataDoubleMatrix(ee, qt, rawMatrix);
    ee = dataUpdater.addData(ee, targetArrayDesign, moreData);
    ee = experimentService.thaw(ee);
    try {
        // add preferred data twice.
        dataUpdater.addData(ee, targetArrayDesign, data);
        fail("Should have gotten an exception");
    } catch (IllegalArgumentException e) {
    // okay.
    }
    dataUpdater.deleteData(ee, qt);
}

Example 2 with DenseDoubleMatrix

use of ubic.basecode.dataStructure.matrix.DenseDoubleMatrix in project Gemma by PavlidisLab.

the class ExpressionDataSVD method equalize.

/**
 * Implements the method described in the SPELL paper, alternative interpretation as related by Q. Morris. Set all
 * components to have equal weight (set all singular values to 1)
 *
 * @return the reconstructed matrix; values that were missing before are re-masked.
 */
public ExpressionDataDoubleMatrix equalize() {
    DoubleMatrix<Integer, Integer> copy = svd.getS().copy();
    for (int i = 0; i < copy.columns(); i++) {
        copy.set(i, i, 1.0);
    }
    double[][] rawU = svd.getU().getRawMatrix();
    double[][] rawS = copy.getRawMatrix();
    double[][] rawV = svd.getV().getRawMatrix();
    DoubleMatrix2D u = new DenseDoubleMatrix2D(rawU);
    DoubleMatrix2D s = new DenseDoubleMatrix2D(rawS);
    DoubleMatrix2D v = new DenseDoubleMatrix2D(rawV);
    Algebra a = new Algebra();
    DoubleMatrix<CompositeSequence, BioMaterial> reconstructed = new DenseDoubleMatrix<>(a.mult(a.mult(u, s), a.transpose(v)).toArray());
    reconstructed.setRowNames(this.expressionData.getMatrix().getRowNames());
    reconstructed.setColumnNames(this.expressionData.getMatrix().getColNames());
    // re-mask the missing values.
    for (int i = 0; i < reconstructed.rows(); i++) {
        for (int j = 0; j < reconstructed.columns(); j++) {
            if (Double.isNaN(this.missingValueInfo.get(i, j))) {
                reconstructed.set(i, j, Double.NaN);
            }
        }
    }
    return new ExpressionDataDoubleMatrix(this.expressionData, reconstructed);
}

Example 3 with DenseDoubleMatrix

use of ubic.basecode.dataStructure.matrix.DenseDoubleMatrix in project Gemma by PavlidisLab.

the class SampleCoexpressionAnalysisDaoImpl method load.

@Override
public DoubleMatrix<BioAssay, BioAssay> load(ExpressionExperiment ee) {
    Collection<SampleCoexpressionMatrix> r = this.findByExperiment(ee);
    if (r.isEmpty())
        return null;
    if (r.size() > 1) {
        AbstractDao.log.warn("More than one matrix was available, only the first is being returned.");
    }
    SampleCoexpressionMatrix matObj = r.iterator().next();
    byte[] matrixBytes = matObj.getCoexpressionMatrix();
    final List<BioAssay> bioAssays = matObj.getBioAssayDimension().getBioAssays();
    int numBa = bioAssays.size();
    if (numBa == 0) {
        throw new IllegalArgumentException("No bioassays in the bioassaydimension with id=" + matObj.getBioAssayDimension().getId());
    }
    double[][] rawMatrix;
    try {
        rawMatrix = SampleCoexpressionAnalysisDaoImpl.bac.byteArrayToDoubleMatrix(matrixBytes, numBa);
    } catch (IllegalArgumentException e) {
        AbstractDao.log.error("EE id = " + ee.getId() + ": " + e.getMessage());
        return null;
    }
    DoubleMatrix<BioAssay, BioAssay> result = new DenseDoubleMatrix<>(rawMatrix);
    try {
        result.setRowNames(bioAssays);
    } catch (IllegalArgumentException e) {
        AbstractDao.log.error("EE id = " + ee.getId() + ": " + e.getLocalizedMessage());
    }
    try {
        result.setColumnNames(bioAssays);
    } catch (IllegalArgumentException e) {
        AbstractDao.log.error("EE id = " + ee.getId() + ": " + e.getLocalizedMessage());
    }
    return result;
}

Example 4 with DenseDoubleMatrix

use of ubic.basecode.dataStructure.matrix.DenseDoubleMatrix in project Gemma by PavlidisLab.

the class SampleCoexpressionMatrixServiceImpl method getMatrix.

private static DoubleMatrix<BioAssay, BioAssay> getMatrix(ExpressionDataDoubleMatrix matrix) {
    DoubleMatrix<BioMaterial, CompositeSequence> transposeR = matrix.getMatrix().transpose();
    DoubleMatrix<BioAssay, CompositeSequence> transpose = new DenseDoubleMatrix<>(transposeR.getRawMatrix());
    transpose.setColumnNames(transposeR.getColNames());
    for (int i = 0; i < transpose.rows(); i++) {
        BioAssay s = transposeR.getRowName(i).getBioAssaysUsedIn().iterator().next();
        transpose.setRowName(s, i);
    }
    return MatrixStats.correlationMatrix(transpose);
}

Example 5 with DenseDoubleMatrix

use of ubic.basecode.dataStructure.matrix.DenseDoubleMatrix in project Gemma by PavlidisLab.

the class ExpressionExperimentBatchCorrectionServiceImpl method doComBat.

private ExpressionDataDoubleMatrix doComBat(ExpressionExperiment ee, ExpressionDataDoubleMatrix originalDataMatrix, ObjectMatrix<BioMaterial, ExperimentalFactor, Object> design) {
    ObjectMatrix<BioMaterial, String, Object> designU = this.convertFactorValuesToStrings(design);
    DoubleMatrix<CompositeSequence, BioMaterial> matrix = originalDataMatrix.getMatrix();
    designU = this.orderMatrix(matrix, designU);
    ScaleType scale = originalDataMatrix.getQuantitationTypes().iterator().next().getScale();
    boolean transformed = false;
    if (!(scale.equals(ScaleType.LOG2) || scale.equals(ScaleType.LOG10) || scale.equals(ScaleType.LOGBASEUNKNOWN) || scale.equals(ScaleType.LN))) {
        ExpressionExperimentBatchCorrectionServiceImpl.log.info(" *** COMBAT: LOG TRANSFORMING ***");
        transformed = true;
        MatrixStats.logTransform(matrix);
    }
    /*
         * Process
         */
    ComBat<CompositeSequence, BioMaterial> comBat = new ComBat<>(matrix, designU);
    // false: NONPARAMETRIC
    DoubleMatrix2D results = comBat.run(true);
    // note these plots always reflect the parametric setup.
    // TEMPORARY?
    comBat.plot(ee.getId() + "." + FileTools.cleanForFileName(ee.getShortName()));
    /*
         * Postprocess. Results is a raw matrix/
         */
    DoubleMatrix<CompositeSequence, BioMaterial> correctedDataMatrix = new DenseDoubleMatrix<>(results.toArray());
    correctedDataMatrix.setRowNames(matrix.getRowNames());
    correctedDataMatrix.setColumnNames(matrix.getColNames());
    if (transformed) {
        MatrixStats.unLogTransform(correctedDataMatrix);
    }
    ExpressionDataDoubleMatrix correctedExpressionDataMatrix = new ExpressionDataDoubleMatrix(originalDataMatrix, correctedDataMatrix);
    assert correctedExpressionDataMatrix.getQuantitationTypes().size() == 1;
    /*
         * It is easier if we make a new quantitationtype.
         */
    QuantitationType oldQt = correctedExpressionDataMatrix.getQuantitationTypes().iterator().next();
    QuantitationType newQt = this.makeNewQuantitationType(oldQt);
    correctedExpressionDataMatrix.getQuantitationTypes().clear();
    correctedExpressionDataMatrix.getQuantitationTypes().add(newQt);
    // Sanity check...
    for (int i = 0; i < correctedExpressionDataMatrix.columns(); i++) {
        assert correctedExpressionDataMatrix.getBioMaterialForColumn(i).equals(originalDataMatrix.getBioMaterialForColumn(i));
    }
    return correctedExpressionDataMatrix;
}