Examples with ColorMatrix ubic.basecode.graphics.ColorMatrix used on opensource projects

Example 1 with ColorMatrix

use of ubic.basecode.graphics.ColorMatrix in project Gemma by PavlidisLab.

the class ExperimentalDesignVisualizationServiceImpl method plotExperimentalDesign.

/**
 * Test method for now, shows how this can be used.
 *
 * @param e ee
 */
// Test method for now, shows how this can be used.
@SuppressWarnings("unused")
protected void plotExperimentalDesign(ExpressionExperiment e) {
    LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> layout = this.getExperimentalDesignLayout(e);
    List<String> efStrings = new ArrayList<>();
    List<String> baStrings = new ArrayList<>();
    List<double[]> rows = new ArrayList<>();
    boolean first = true;
    int i = 0;
    for (BioAssayValueObject ba : layout.keySet()) {
        baStrings.add(ba.getName());
        int j = 0;
        for (ExperimentalFactor ef : layout.get(ba).keySet()) {
            if (first) {
                double[] nextRow = new double[layout.size()];
                rows.add(nextRow);
                // make sure they are unique.
                efStrings.add(ef.getName() + " ( id=" + ef.getId() + ")");
            }
            double d = layout.get(ba).get(ef);
            rows.get(j)[i] = d;
            j++;
        }
        i++;
        first = false;
    }
    double[][] mat = rows.toArray(new double[][] {});
    DoubleMatrix<String, String> data = DoubleMatrixFactory.dense(mat);
    data.setRowNames(efStrings);
    data.setColumnNames(baStrings);
    ColorMatrix<String, String> cm = new ColorMatrix<>(data, ColorMap.GREENRED_COLORMAP, Color.GRAY);
    try {
        this.writeImage(cm, File.createTempFile(e.getShortName() + "_", ".png"));
    } catch (IOException e1) {
        throw new RuntimeException(e1);
    }
}

Example 2 with ColorMatrix

use of ubic.basecode.graphics.ColorMatrix in project Gemma by PavlidisLab.

the class ExpressionExperimentQCController method visualizeCorrMat.

/**
 * @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 showLabels if the row and column labels of the matrix should be shown.
 * @param os         response output stream
 */
@RequestMapping("/expressionExperiment/visualizeCorrMat.html")
public ModelAndView visualizeCorrMat(Long id, Double size, String contrVal, Boolean text, Boolean showLabels, Boolean forceShowLabels, 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;
    }
    DoubleMatrix<BioAssay, BioAssay> omatrix = sampleCoexpressionMatrixService.findOrCreate(ee);
    List<String> stringNames = new ArrayList<>();
    for (BioAssay ba : omatrix.getRowNames()) {
        stringNames.add(ba.getName() + " ID=" + ba.getId());
    }
    DoubleMatrix<String, String> matrix = new DenseDoubleMatrix<>(omatrix.getRawMatrix());
    matrix.setRowNames(stringNames);
    matrix.setColumnNames(stringNames);
    if (text != null && text) {
        StringWriter s = new StringWriter();
        MatrixWriter<String, String> mw = new MatrixWriter<>(s, new DecimalFormat("#.##"));
        mw.writeMatrix(matrix, true);
        ModelAndView mav = new ModelAndView(new TextView());
        mav.addObject(TextView.TEXT_PARAM, s.toString());
        return mav;
    }
    /*
         * Blank out the diagonal so it doesn't affect the colour scale.
         */
    for (int i = 0; i < matrix.rows(); i++) {
        matrix.set(i, i, Double.NaN);
    }
    ColorMatrix<String, String> cm = new ColorMatrix<>(matrix);
    this.cleanNames(matrix);
    int row = matrix.rows();
    int cellsize = (int) Math.min(ExpressionExperimentQCController.MAX_HEATMAP_CELLSIZE, Math.max(1, size * ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX / row));
    MatrixDisplay<String, String> writer = new MatrixDisplay<>(cm);
    boolean reallyShowLabels;
    int minimumCellSizeForText = 9;
    if (forceShowLabels != null && forceShowLabels) {
        cellsize = Math.min(ExpressionExperimentQCController.MAX_HEATMAP_CELLSIZE, minimumCellSizeForText);
        reallyShowLabels = true;
    } else {
        reallyShowLabels = showLabels != null && (showLabels && cellsize >= minimumCellSizeForText);
    }
    writer.setCellSize(new Dimension(cellsize, cellsize));
    boolean showScalebar = size > 2;
    writer.writeToPng(cm, os, reallyShowLabels, showScalebar);
    // nothing to return;
    return null;
}