Examples with ColorGradientRange org.mskcc.colorgradient.ColorGradientRange used on opensource projects

Example 1 with ColorGradientRange

use of org.mskcc.colorgradient.ColorGradientRange in project EnrichmentMapApp by BaderLab.

the class DataSetColorRange method create.

/**
	 * Reset color gradients based on a change in the data transformation.
	 */
public static DataSetColorRange create(EMDataSet ds, Transform transform) {
    GeneExpressionMatrix expression = ds.getExpressionSets();
    double minExpression = expression.getMinExpression();
    double maxExpression = expression.getMaxExpression();
    double min;
    double max;
    switch(transform) {
        case AS_IS:
        default:
            min = minExpression;
            max = Math.max(Math.abs(minExpression), maxExpression);
            break;
        case ROW_NORMALIZE:
            min = expression.getMinExpression(expression.getExpressionMatrix_rowNormalized());
            max = expression.getMaxExpression(expression.getExpressionMatrix_rowNormalized());
            //This happens when there is only one data column in the dataset (or if it is rank file)
            if ((min == 0) && (max == 0)) {
            //JOptionPane.showMessageDialog(Cytoscape.getDesktop(),"Row normalization does not work with only one data column per dataset.","Row normalization error",JOptionPane.WARNING_MESSAGE);
            }
            max = Math.max(Math.abs(min), max);
            break;
        case LOG_TRANSFORM:
            //issue a warning.
            if ((minExpression <= 0) && (maxExpression <= 0)) {
                //both the max and min are probably negative values
                //JOptionPane.showMessageDialog(Cytoscape.getDesktop(),"Both the max and min expression are negative, log of negative numbers is not valid", "log normalization error", JOptionPane.WARNING_MESSAGE);
                min = 0;
                max = 0;
            } else //if min expression is negative then use the max expression as the max
            if (minExpression <= 0) {
                double closestToZeroExpression = expression.getClosesttoZero();
                min = Math.min(Math.log(closestToZeroExpression), Math.log1p(maxExpression));
                max = Math.max(Math.log(closestToZeroExpression), Math.log1p(maxExpression));
            } else //if the max expression is negative then use the min expression as the max (should never happen!)
            if (maxExpression <= 0) {
                min = 0;
                max = Math.log1p(minExpression);
            } else {
                min = Math.log1p(minExpression);
                max = Math.log1p(maxExpression);
                max = Math.max(Math.abs(min), max);
            }
            break;
    }
    if (min >= 0) {
        double median = max / 2;
        ColorGradientRange range = ColorGradientRange.getInstance(0, median, median, max, 0, median, median, max);
        ColorGradientTheme theme = ColorGradientTheme.GREEN_ONECOLOR_GRADIENT_THEME;
        return new DataSetColorRange(theme, range);
    } else {
        ColorGradientRange range = ColorGradientRange.getInstance(-max, 0, 0, max, -max, 0, 0, max);
        ColorGradientTheme theme = ColorGradientTheme.PR_GN_GRADIENT_THEME;
        return new DataSetColorRange(theme, range);
    }
}