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

Example 71 with DoubleMatrix2D

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

the class ComBatTest method test3NoCovariate.

/*
     * Case where we only have batch, no other covariates
     *
     */
@Test
public void test3NoCovariate() throws Exception {
    DoubleMatrixReader f = new DoubleMatrixReader();
    DoubleMatrix<String, String> testMatrix = f.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/example.madata.small.txt"));
    StringMatrixReader of = new StringMatrixReader();
    StringMatrix<String, String> sampleInfo = of.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/example.metadata.nocov.small.txt"));
    @SuppressWarnings({ "unchecked", "rawtypes" }) ComBat<String, String> comBat = new ComBat(testMatrix, sampleInfo);
    DoubleMatrix2D X = comBat.getDesignMatrix();
    assertEquals(1, X.get(0, 0), 0.001);
    assertEquals(0, X.get(3, 0), 0.001);
    DoubleMatrix2D y = new DenseDoubleMatrix2D(testMatrix.asArray());
    DoubleMatrix2D sdata = comBat.standardize(y, X);
    assertEquals(-0.57397393, sdata.get(17, 1), 0.0001);
    assertEquals(1.10827459, sdata.get(8, 2), 0.001);
    assertEquals(0.45359207, sdata.get(0, 8), 0.001);
    assertEquals(0.15470664, sdata.get(3, 7), 0.001);
    DoubleMatrix2D finalResult = comBat.run();
    assertEquals(10.678412, finalResult.get(7, 0), 0.0001);
    assertEquals(11.677158, finalResult.get(7, 7), 0.0001);
    assertEquals(6.735682, finalResult.get(10, 7), 0.0001);
// log.info( finalResult );
// X08.1 X54.1 X36.1 X23.1 X17.1 X40.1 X45.1 X55.1 X11.1
// 1553129_at 3.862883 3.666102 3.891911 3.968716 3.920277 3.854683 3.879281 3.837050 3.858994
// 213447_at 6.233228 5.393208 5.601587 6.008113 6.456638 6.170673 5.312780 4.707229 6.568215
// 242039_at 8.164096 8.502608 7.550607 7.146657 7.549429 7.914666 8.128463 8.437540 7.919430
// 223394_at 7.785804 8.172181 8.258501 8.286628 7.847273 8.259993 8.611244 8.164748 7.386591
// 227758_at 3.816278 3.475673 3.642967 3.670807 3.694009 3.641609 3.641609 3.633687 3.958491
// 207696_at 3.580712 3.527869 3.565008 3.518815 3.510254 3.589519 3.624747 3.666631 3.601962
// 241107_at 6.256698 5.922966 5.679003 5.749597 6.179683 5.589234 5.529333 5.900868 6.405107
// 228980_at 10.678412 11.107177 10.773365 10.974208 10.592659 11.793201 10.935671 11.677158 10.572522
// 204452_s_at 6.021874 5.366750 5.931940 6.337327 5.712018 5.260514 5.650047 5.355390 5.562588
// 1562443_at 4.609301 3.964679 4.663442 4.516068 4.818594 4.140485 4.232574 4.084472 4.684495
// 232018_at 6.226565 6.878310 6.097034 5.956156 5.989567 6.497420 6.929095 6.735682 5.721358
// 1561877_at 3.789971 3.749341 3.728529 3.867675 4.058129 3.659954 3.473056 3.856079 3.879270
// 221183_at 6.790431 5.543900 6.253127 6.541754 6.737387 5.703031 6.065498 5.210347 7.035212
// 206162_x_at 5.294347 5.257304 5.090348 4.979353 5.118390 5.544392 5.553653 5.884388 5.542866
// 214502_at 4.047479 3.865124 3.805045 3.963706 3.906569 4.478499 3.972879 4.154100 3.752158
// 234099_at 7.596681 6.861572 7.109911 6.946028 7.208003 6.455995 6.641884 6.761660 7.703987
// 237400_at 4.437312 5.820944 5.026344 4.825555 5.319276 5.731938 4.582957 4.979099 4.860988
// 240254_at 4.106446 3.903017 4.238474 4.121097 4.000663 6.213980 4.057623 3.815918 4.484964
// 209053_s_at 5.979671 6.378071 6.241459 6.440983 5.946471 6.685171 6.452771 6.374475 5.986512
}

Example 72 with DoubleMatrix2D

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

the class ComBatTest method test1.

@Test
public void test1() throws Exception {
    DoubleMatrixReader f = new DoubleMatrixReader();
    DoubleMatrix<String, String> testMatrix = f.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/example.madata.small.txt"));
    StringMatrixReader of = new StringMatrixReader();
    StringMatrix<String, String> sampleInfo = of.read(this.getClass().getResourceAsStream("/data/analysis/preprocess/batcheffects/example.metadata.small.txt"));
    @SuppressWarnings({ "unchecked", "rawtypes" }) ComBat<String, String> comBat = new ComBat(testMatrix, sampleInfo);
    DoubleMatrix2D X = comBat.getDesignMatrix();
    assertEquals(1, X.get(0, 0), 0.001);
    assertEquals(0, X.get(3, 0), 0.001);
    assertEquals(1, X.get(4, 2), 0.001);
    DoubleMatrix2D y = new DenseDoubleMatrix2D(testMatrix.asArray());
    DoubleMatrix2D sdata = comBat.standardize(y, X);
    assertEquals(-0.25074, sdata.get(17, 1), 0.0001);
    assertEquals(0.54122, sdata.get(8, 2), 0.001);
    assertEquals(0.22358, sdata.get(0, 8), 0.001);
    assertEquals(0.25211, sdata.get(3, 7), 0.001);
    DoubleMatrix2D finalResult = comBat.run();
    assertEquals(10.67558, finalResult.get(7, 0), 0.0001);
    assertEquals(11.68505, finalResult.get(7, 7), 0.0001);
    assertEquals(6.769583, finalResult.get(10, 7), 0.0001);
}

Example 73 with DoubleMatrix2D

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

the class ExpressionExperimentQCController method visualizeMeanVariance.

/**
 * @param id   of experiment
 * @param size Multiplier on the cell size. 1 or null for standard small size.
 * @param text if true, output a tabbed file instead of a png
 * @param os   response output stream
 * @return ModelAndView object if text is true, otherwise null
 */
@RequestMapping("/expressionExperiment/visualizeMeanVariance.html")
public ModelAndView visualizeMeanVariance(Long id, Double size, Boolean text, OutputStream os) throws Exception {
    if (id == null) {
        log.warn("No id!");
        return null;
    }
    ExpressionExperiment ee = expressionExperimentService.load(id);
    if (ee == null) {
        log.warn("Could not load experiment with id " + id);
        return null;
    }
    MeanVarianceRelation mvr = meanVarianceService.find(ee);
    if (mvr == null) {
        return null;
    }
    if (text != null && text) {
        final ByteArrayConverter bac = new ByteArrayConverter();
        double[] means = bac.byteArrayToDoubles(mvr.getMeans());
        double[] variances = bac.byteArrayToDoubles(mvr.getVariances());
        DoubleMatrix2D matrix = new DenseDoubleMatrix2D(means.length, 2);
        matrix.viewColumn(0).assign(means);
        matrix.viewColumn(1).assign(variances);
        String matrixString = new Formatter("%1.2G").toTitleString(matrix, null, new String[] { "mean", "variance" }, null, null, null, null);
        ModelAndView mav = new ModelAndView(new TextView());
        mav.addObject(TextView.TEXT_PARAM, matrixString);
        return mav;
    }
    this.writeMeanVariance(os, mvr, size);
    return null;
}

Example 74 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project tdq-studio-se by Talend.

the class Formatter method demo4.

/**
 * Demonstrates how to use this class.
 */
public static void demo4() {
    // parameters
    double[][] values = { { 3, 0, -3.4, 0 }, { 5.1, 0, +3.0123456789, 0 }, { 16.37, 0.0, 2.5, 0 }, { -16.3, 0, -3.012345678E-4, -1 }, { 1236.3456789, 0, 7, -1.2 } };
    /*
double[][] values = {
	{3,     1,      },
	{5.1   ,16.37,  }
};
*/
    // String[] columnNames = { "he",   "",  "he", "four" };
    // String[] rowNames = { "hello", "du", null, "abcdef", "five" };
    String[] columnNames = { "0.1", "0.3", "0.5", "0.7" };
    String[] rowNames = { "SunJDK1.2.2 classic", "IBMJDK1.1.8", "SunJDK1.3 Hotspot", "other1", "other2" };
    // String[] columnNames = { "0.1", "0.3" };
    // String[] rowNames = { "SunJDK1.2.2 classic", "IBMJDK1.1.8"};
    DoubleMatrix2D matrix = cern.colt.matrix.DoubleFactory2D.dense.make(values);
    System.out.println("\n\n" + new Formatter("%G").toTitleString(matrix, rowNames, columnNames, "rowAxis", "colAxis", "VM Performance: Provider vs. matrix density"));
}

Example 75 with DoubleMatrix2D

use of cern.colt.matrix.DoubleMatrix2D in project tdq-studio-se by Talend.

the class Formatter method demo3.

/**
 * Demonstrates how to use this class.
 */
public static void demo3(int size, double value) {
    cern.colt.Timer timer = new cern.colt.Timer();
    String s;
    StringBuffer buf;
    DoubleMatrix2D matrix = cern.colt.matrix.DoubleFactory2D.dense.make(size, size, value);
    timer.reset().start();
    buf = new StringBuffer();
    for (int i = size; --i >= 0; ) {
        for (int j = size; --j >= 0; ) {
            buf.append(matrix.getQuick(i, j));
        }
    }
    buf = null;
    timer.stop().display();
    timer.reset().start();
    cern.colt.matrix.impl.Former format = new cern.colt.matrix.impl.FormerFactory().create("%G");
    buf = new StringBuffer();
    for (int i = size; --i >= 0; ) {
        for (int j = size; --j >= 0; ) {
            buf.append(format.form(matrix.getQuick(i, j)));
        }
    }
    buf = null;
    timer.stop().display();
    timer.reset().start();
    s = new Formatter(null).toString(matrix);
    // System.out.println(s);
    s = null;
    timer.stop().display();
    timer.reset().start();
    s = new Formatter("%G").toString(matrix);
    // System.out.println(s);
    s = null;
    timer.stop().display();
}