Example usage for org.jfree.chart.plot CombinedRangeXYPlot getSubplots

Introduction

In this page you can find the example usage for org.jfree.chart.plot CombinedRangeXYPlot getSubplots.

Prototype

public List getSubplots()

Source Link

Document

Returns the list of subplots.

Usage

From source file:org.gwaspi.reports.PlinkReportLoaderCombined.java

private static void appendToCombinedRangePlot(CombinedRangeXYPlot combinedPlot, String chromosome,
        XYSeriesCollection tempChrData, boolean showlables) {
    XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(false, true);
    renderer.setSeriesPaint(0, Color.blue);
    renderer.setSeriesPaint(1, Color.red);
    renderer.setSeriesVisibleInLegend(0, showlables);
    renderer.setSeriesVisibleInLegend(1, showlables);
    //renderer.setBaseShape(new Ellipse2D.Float(0, 0, 2,2), false);

    if (combinedPlot.getSubplots().isEmpty()) {
        LogAxis rangeAxis = new LogAxis("P value");
        rangeAxis.setBase(10);//from   w ww.j a va 2  s .  c o m
        rangeAxis.setInverted(true);
        rangeAxis.setNumberFormatOverride(GenericReportGenerator.FORMAT_P_VALUE);

        rangeAxis.setTickMarkOutsideLength(2.0f);
        rangeAxis.setMinorTickCount(2);
        rangeAxis.setMinorTickMarksVisible(true);
        rangeAxis.setAxisLineVisible(true);
        rangeAxis.setAutoRangeMinimumSize(0.0000005);
        rangeAxis.setLowerBound(1d);
        //rangeAxis.setAutoRangeIncludesZero(false);

        combinedPlot.setRangeAxis(0, rangeAxis);
    }

    JFreeChart subchart = ChartFactory.createScatterPlot("", "Chr " + chromosome, "", tempChrData,
            PlotOrientation.VERTICAL, true, false, false);

    XYPlot subplot = (XYPlot) subchart.getPlot();
    subplot.setRenderer(renderer);
    subplot.setBackgroundPaint(null);

    final Marker thresholdLine = new ValueMarker(0.0000005);
    thresholdLine.setPaint(Color.red);
    if (showlables) {
        thresholdLine.setLabel("P = 510??");
    }
    thresholdLine.setLabelAnchor(RectangleAnchor.TOP_RIGHT);
    thresholdLine.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT);
    subplot.addRangeMarker(thresholdLine);

    NumberAxis chrAxis = (NumberAxis) subplot.getDomainAxis();
    chrAxis.setAxisLineVisible(false);
    chrAxis.setTickLabelsVisible(false);
    chrAxis.setTickMarksVisible(false);
    chrAxis.setAutoRangeIncludesZero(false);
    //combinedPlot.setGap(0);
    combinedPlot.add(subplot, 1);
}

From source file:org.gwaspi.reports.GenericReportGenerator.java

private static void appendToCombinedRangeManhattanPlot(CombinedRangeXYPlot combinedPlot, String chromosome,
        XYSeriesCollection currChrSC, boolean showlables, double threshold, Color background,
        Color backgroundAlternative, Color main) {

    XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(false, true);

    // Set dot shape of the currently appended Series
    renderer.setSeriesPaint(currChrSC.getSeriesCount() - 1, main);
    renderer.setSeriesVisibleInLegend(currChrSC.getSeriesCount() - 1, showlables);
    renderer.setSeriesShape(currChrSC.getSeriesCount() - 1, new Rectangle2D.Double(-1.0, -1.0, 2.0, 2.0));

    // Set range axis
    if (combinedPlot.getSubplots().isEmpty()) {
        LogAxis rangeAxis = new LogAxis("P value");
        rangeAxis.setBase(10);//from w  w w  .  jav a2 s  .  c o m
        rangeAxis.setInverted(true);
        rangeAxis.setNumberFormatOverride(FORMAT_P_VALUE);

        rangeAxis.setTickMarkOutsideLength(2.0f);
        rangeAxis.setMinorTickCount(2);
        rangeAxis.setMinorTickMarksVisible(true);
        rangeAxis.setAxisLineVisible(true);
        rangeAxis.setUpperMargin(0);

        TickUnitSource units = NumberAxis.createIntegerTickUnits();
        rangeAxis.setStandardTickUnits(units);

        combinedPlot.setRangeAxis(0, rangeAxis);
    }

    // Build subchart
    JFreeChart subchart = ChartFactory.createScatterPlot("", "Chr " + chromosome, "", currChrSC,
            PlotOrientation.VERTICAL, false, false, false);

    // Get subplot from subchart
    XYPlot subplot = (XYPlot) subchart.getPlot();
    subplot.setRenderer(renderer);
    subplot.setBackgroundPaint(null);

    // CHART BACKGROUD COLOR
    if (combinedPlot.getSubplots().size() % 2 == 0) {
        subplot.setBackgroundPaint(background); // Hue, saturation, brightness
    } else {
        subplot.setBackgroundPaint(backgroundAlternative); // Hue, saturation, brightness
    }

    // Add significance Threshold to subplot
    final Marker thresholdLine = new ValueMarker(threshold);
    thresholdLine.setPaint(Color.red);
    // Add legend to hetzyThreshold
    if (showlables) {
        thresholdLine.setLabel("P = " + FORMAT_P_VALUE.format(threshold));
    }
    thresholdLine.setLabelAnchor(RectangleAnchor.TOP_RIGHT);
    thresholdLine.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT);
    subplot.addRangeMarker(thresholdLine);

    // Chromosome Axis Labels
    NumberAxis chrAxis = (NumberAxis) subplot.getDomainAxis();
    chrAxis.setLabelAngle(1.0);
    chrAxis.setAutoRangeIncludesZero(false);
    chrAxis.setAxisLineVisible(true);

    chrAxis.setTickLabelsVisible(false);
    chrAxis.setTickMarksVisible(false);
    //      chrAxis.setNumberFormatOverride(Report_Analysis.FORMAT_SCIENTIFIC);
    //      TickUnitSource units = NumberAxis.createIntegerTickUnits();
    //      chrAxis.setStandardTickUnits(units);

    //combinedPlot.setGap(0);
    combinedPlot.add(subplot, 1);
}