Examples with DoubleMatrix2D cern.colt.matrix.DoubleMatrix2D used on opensource projects

Example 56 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBatTest method test5NonParametric.

@Test
public void test5NonParametric() throws Exception {
    DoubleMatrixReader f = new DoubleMatrixReader();
    DoubleMatrix<String, String> testMatrix = f.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/GSE492.test.dat.txt"));
    StringMatrixReader of = new StringMatrixReader();
    StringMatrix<String, String> sampleInfo = of.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/100_GSE492_expdesign.data.txt"));
    @SuppressWarnings({ "unchecked", "rawtypes" }) ComBat<String, String> comBat = new ComBat(testMatrix, sampleInfo);
    DoubleMatrix2D X = comBat.getDesignMatrix();
    // log.info( X );
    assertEquals(1, X.get(0, 0), 0.001);
    assertEquals(0, X.get(1, 0), 0.001);
    assertEquals(0, X.get(4, 3), 0.001);
    DoubleMatrix2D y = new DenseDoubleMatrix2D(testMatrix.asArray());
    DoubleMatrix2D sdata = comBat.standardize(y, X);
    // log.info( sdata.viewPart( 0, 0, 10, 12 ) );
    assertEquals(-1.85175902, sdata.get(7, 1), 0.0001);
    assertEquals(0.2479669, sdata.get(8, 2), 0.001);
    assertEquals(-0.56259384, sdata.get(0, 8), 0.001);
    assertEquals(1.07168246, sdata.get(3, 11), 0.001);
    DoubleMatrix2D finalResult = comBat.run(false);
    assertEquals(12.026930, finalResult.get(7, 0), 0.001);
    assertEquals(11.635157, finalResult.get(7, 7), 0.01);
    assertEquals(12.930425, finalResult.get(9, 7), 0.01);
}

Example 57 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBatTest method test3.

/**
 * Based on GSE13712
 */
@Test
public final void test3() throws Exception {
    DoubleMatrixReader f = new DoubleMatrixReader();
    DoubleMatrix<String, String> testMatrix = f.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/comat.test.data.txt"));
    StringMatrixReader of = new StringMatrixReader();
    StringMatrix<String, String> sampleInfo = of.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/combat.test.design.txt"));
    @SuppressWarnings({ "unchecked", "rawtypes" }) ComBat<String, String> comBat = new ComBat(testMatrix, sampleInfo);
    DoubleMatrix2D result = comBat.run();
    assertNotNull(result);
}

Example 58 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project Gemma by PavlidisLab.

the class ComBatTest method test4.

@Test
public void test4() throws Exception {
    DoubleMatrixReader f = new DoubleMatrixReader();
    DoubleMatrix<String, String> testMatrix = f.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/GSE492.test.dat.txt"));
    StringMatrixReader of = new StringMatrixReader();
    ObjectMatrix<String, String, String> sampleInfo = of.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/100_GSE492_expdesign.data.txt"));
    @SuppressWarnings({ "unchecked", "rawtypes" }) ComBat<String, String> comBat = new ComBat(testMatrix, sampleInfo);
    DoubleMatrix2D X = comBat.getDesignMatrix();
    // log.info( X );
    assertEquals(1, X.get(0, 0), 0.001);
    assertEquals(0, X.get(1, 0), 0.001);
    assertEquals(0, X.get(4, 3), 0.001);
    DoubleMatrix2D y = new DenseDoubleMatrix2D(testMatrix.asArray());
    DoubleMatrix2D sdata = comBat.standardize(y, X);
    // log.info( sdata.viewPart( 0, 0, 10, 12 ) );
    assertEquals(-1.85175902, sdata.get(7, 1), 0.0001);
    assertEquals(0.2479669, sdata.get(8, 2), 0.001);
    assertEquals(-0.56259384, sdata.get(0, 8), 0.001);
    assertEquals(1.07168246, sdata.get(3, 11), 0.001);
    DoubleMatrix2D finalResult = comBat.run();
    assertEquals(12.026468, finalResult.get(7, 0), 0.0001);
    assertEquals(11.640057, finalResult.get(7, 7), 0.0001);
    assertEquals(12.932352, finalResult.get(9, 7), 0.0001);
}

Example 59 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project midpoint by Evolveum.

the class AbstractOrgClosureTest method checkClosureMatrix.

protected boolean checkClosureMatrix() throws SchemaException {
    try (Session session = openSession()) {
        // we compute the closure table "by hand" as 1 + A + A^2 + A^3 + ... + A^n where n is the greatest expected path length
        int vertices = getVertices().size();
        long start = System.currentTimeMillis();
        // used to give indices to vertices
        List<String> vertexList = new ArrayList<>(getVertices());
        if (DUMP_TC_MATRIX_DETAILS) {
            logger.info("Vertex list = {}", vertexList);
        }
        DoubleMatrix2D a = new SparseDoubleMatrix2D(vertices, vertices);
        // }
        for (DefaultEdge edge : orgGraph.edgeSet()) {
            a.set(vertexList.indexOf(orgGraph.getEdgeSource(edge)), vertexList.indexOf(orgGraph.getEdgeTarget(edge)), 1.0);
        }
        DoubleMatrix2D result = new SparseDoubleMatrix2D(vertices, vertices);
        for (int i = 0; i < vertices; i++) {
            result.setQuick(i, i, 1.0);
        }
        DoubleMatrix2D power = result.copy();
        Algebra alg = new Algebra();
        for (int level = 1; level <= maxLevel; level++) {
            power = alg.mult(power, a);
            result.assign(power, Functions.plus);
        // System.out.println("a=" + a);
        // System.out.println("a^"+level+"="+power);
        }
        logger.info("TC matrix computed in {} ms", System.currentTimeMillis() - start);
        if (DUMP_TC_MATRIX_DETAILS) {
            logger.info("TC matrix expected = {}", result);
        }
        Query q = session.createNativeQuery("select descendant_oid, ancestor_oid, val from m_org_closure").addScalar("descendant_oid", StringType.INSTANCE).addScalar("ancestor_oid", StringType.INSTANCE).addScalar("val", LongType.INSTANCE);
        List<Object[]> list = q.list();
        logger.info("OrgClosure has {} rows", list.size());
        DoubleMatrix2D closureInDatabase = new SparseDoubleMatrix2D(vertices, vertices);
        for (Object[] item : list) {
            int val = Integer.parseInt(item[2].toString());
            if (val == 0) {
                throw new IllegalStateException("Row with val == 0 in closure table: " + list);
            }
            closureInDatabase.set(vertexList.indexOf(item[0]), vertexList.indexOf(item[1]), val);
        }
        if (DUMP_TC_MATRIX_DETAILS) {
            logger.info("TC matrix fetched from db = {}", closureInDatabase);
        }
        double zSumResultBefore = result.zSum();
        double zSumClosureInDb = closureInDatabase.zSum();
        result.assign(closureInDatabase, Functions.minus);
        double zSumResultAfter = result.zSum();
        logger.info("Summary of items in closure computed: {}, in DB-stored closure: {}, delta: {}", zSumResultBefore, zSumClosureInDb, zSumResultAfter);
        if (DUMP_TC_MATRIX_DETAILS) {
            logger.info("Difference matrix = {}", result);
        }
        boolean problem = false;
        for (int i = 0; i < vertices; i++) {
            for (int j = 0; j < vertices; j++) {
                double delta = result.get(i, j);
                if (Math.round(delta) != 0) {
                    System.err.println("delta(" + vertexList.get(i) + "," + vertexList.get(j) + ") = " + delta + " (closureInDB=" + closureInDatabase.get(i, j) + ", expected=" + (result.get(i, j) + closureInDatabase.get(i, j)) + ")");
                    logger.error("delta(" + vertexList.get(i) + "," + vertexList.get(j) + ") = " + delta);
                    problem = true;
                }
            }
        }
        if (problem) {
            checkOrgGraph();
        }
        return problem;
    }
}

Example 60 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project beast-mcmc by beast-dev.

the class MarkovModulatedFrequencyModel method computeStationaryDistribution.

private void computeStationaryDistribution(double[] statDistr) {
    if (allRatesAreZero(switchingRates)) {
        return;
    }
    // Uses an LU decomposition to solve Q^t \pi = 0 and \sum \pi_i = 1
    DoubleMatrix2D mat2 = new DenseDoubleMatrix2D(numBaseModel + 1, numBaseModel);
    int index2 = 0;
    for (int i = 0; i < numBaseModel; ++i) {
        for (int j = i + 1; j < numBaseModel; ++j) {
            // Transposed
            mat2.set(j, i, switchingRates.getParameterValue(index2));
            index2++;
        }
    }
    for (int j = 0; j < numBaseModel; ++j) {
        for (int i = j + 1; i < numBaseModel; ++i) {
            // Transposed
            mat2.set(j, i, switchingRates.getParameterValue(index2));
            index2++;
        }
    }
    for (int i = 0; i < numBaseModel; ++i) {
        double rowTotal = 0.0;
        for (int j = 0; j < numBaseModel; ++j) {
            if (i != j) {
                // Transposed
                rowTotal += mat2.get(j, i);
            }
        }
        mat2.set(i, i, -rowTotal);
    }
    // Add row for sum-to-one constraint
    for (int i = 0; i < numBaseModel; ++i) {
        mat2.set(numBaseModel, i, 1.0);
    }
    LUDecomposition decomp = new LUDecomposition(mat2);
    DoubleMatrix2D x = new DenseDoubleMatrix2D(numBaseModel + 1, 1);
    x.set(numBaseModel, 0, 1.0);
    DoubleMatrix2D y = decomp.solve(x);
    for (int i = 0; i < numBaseModel; ++i) {
        statDistr[i] = y.get(i, 0);
    }
//System.err.println(new Vector(statDistr));              
}