Examples with DoubleArrayList cern.colt.list.DoubleArrayList used on opensource projects

Example 46 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class DoubleVectorValueObject method standardize.

/**
 * @return data adjusted to mean 0, variance 1.
 */
public double[] standardize() {
    /*
         * FIXME If the values are all equal, variance == 0 and we get nothing back. So we should fill in zeros instead.
         */
    /*
         * DoubleArrayList constructor does not make a copy, so we have to make one.
         */
    double[] copy = new double[this.data.length];
    System.arraycopy(data, 0, copy, 0, data.length);
    DescriptiveWithMissing.standardize(new DoubleArrayList(copy));
    return copy;
}

Example 47 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class GeneCoexpressionNodeDegreeValueObject method asDoubleArray.

private double[] asDoubleArray(TreeMap<Integer, Double> map) {
    DoubleArrayList list = new DoubleArrayList();
    if (map.isEmpty())
        return this.toPrimitive(list);
    list.setSize(Math.max(list.size(), map.lastKey() + 1));
    for (Integer s : map.keySet()) {
        list.set(s, map.get(s));
    }
    return this.toPrimitive(list);
}

Example 48 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class ExpressionDataMatrixServiceImpl method getRankMatrix.

@Override
public DoubleMatrix<Gene, ExpressionExperiment> getRankMatrix(Collection<Gene> genes, Collection<ExpressionExperiment> ees, ProcessedExpressionDataVectorDao.RankMethod method) {
    DoubleMatrix<Gene, ExpressionExperiment> matrix = new DenseDoubleMatrix<>(genes.size(), ees.size());
    Map<ExpressionExperiment, Map<Gene, Collection<Double>>> ranks = processedExpressionDataVectorService.getRanks(ees, genes, method);
    matrix.setRowNames(new ArrayList<>(genes));
    matrix.setColumnNames(new ArrayList<>(ees));
    for (int i = 0; i < matrix.rows(); i++) {
        for (int j = 0; j < matrix.columns(); j++) {
            matrix.setByKeys(matrix.getRowName(i), matrix.getColName(j), Double.NaN);
        }
    }
    for (Gene g : matrix.getRowNames()) {
        for (ExpressionExperiment e : matrix.getColNames()) {
            if (ranks.containsKey(e)) {
                Collection<Double> r = ranks.get(e).get(g);
                if (r == null) {
                    continue;
                }
                Double[] ar = r.toArray(new Double[r.size()]);
                // compute median of collection.
                double[] dar = ArrayUtils.toPrimitive(ar);
                double medianRank = DescriptiveWithMissing.median(new DoubleArrayList(dar));
                matrix.setByKeys(g, e, medianRank);
            }
        }
    }
    return matrix;
}

Example 49 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class SpearmanMetricsTest method testCorrel.

/**
 * Value from R; this has ties.
 * <pre>
 * &gt; a&lt;-c(49.0, 43.0, 310.0, 20.0, 20.0, 688.0, 498.0, 533.0, 723.0, 1409.0,279.0);
 * &gt; b&lt;-c(1545.0, 1287.0, 2072.0, 1113.0, 676.0, 2648.0, 2478.0, 2574.0, 3554.0,5155.0, 1624.0);
 * &gt; cor(a,b, method=&quot;spearman&quot;);
 * [1] 0.9977247
 * </pre>
 */
@Test
public void testCorrel() {
    // note the nominal tie in one (20)
    double[] a = new double[] { 49.0, 43.0, 310.0, 20.0, 20.0, 688.0, 498.0, 533.0, 723.0, 1409.0, 279.0 };
    double[] b = new double[] { 1545.0, 1287.0, 2072.0, 1113.0, 676.0, 2648.0, 2478.0, 2574.0, 3554.0, 5155.0, 1624.0 };
    boolean[] usedA = new boolean[] { true, true, true, true, true, true, true, true, true, true, true };
    boolean[] usedB = new boolean[] { true, true, true, true, true, true, true, true, true, true, true };
    assertEquals(a.length, usedA.length);
    assertEquals(b.length, usedB.length);
    DoubleArrayList ranksIA = Rank.rankTransform(new DoubleArrayList(a));
    DoubleArrayList ranksIB = Rank.rankTransform(new DoubleArrayList(b));
    SpearmanMetrics test = new SpearmanMetrics(10);
    double actualValue = test.spearman(ranksIA.elements(), ranksIB.elements(), usedA, usedB, 0, 1);
    double expectedValue = 0.9977247;
    assertEquals(expectedValue, actualValue, 0.0001);
}

Example 50 with DoubleArrayList

use of cern.colt.list.DoubleArrayList in project Gemma by PavlidisLab.

the class SpearmanMetricsTest method testCorrelC.

/**
 * Without missing values, fast method (same data as testCorrelB)
 */
@Test
public void testCorrelC() {
    double[] a = new double[] { 400, 310, 20, 20, 688, 498, 533, 1409, 1500 };
    double[] b = new double[] { 1545, 2072, 1113, 676, 2648, 2478, 2574, 5155, 1624 };
    assertEquals(a.length, b.length);
    DoubleArrayList ranksIA = Rank.rankTransform(new DoubleArrayList(a));
    DoubleArrayList ranksIB = Rank.rankTransform(new DoubleArrayList(b));
    SpearmanMetrics test = new SpearmanMetrics(10);
    double actualValue = test.correlFast(ranksIA.elements(), ranksIB.elements(), 7.713624, 7.745967, 5, 5);
    double expectedValue = 0.7113033;
    assertEquals(expectedValue, actualValue, 0.0001);
}