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

Introduction

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

Prototype

public void setFixedLegendItems(LegendItemCollection items) 

Source Link

Document

Sets the fixed legend items for the plot.

Usage

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

public static CombinedRangeXYPlot buildManhattanPlot(OperationKey testOpKey) throws IOException {

    // PLOT DEFAULTS
    final Config config = Config.getSingleton();
    final double threshold = config.getDouble(PLOT_MANHATTAN_THRESHOLD_CONFIG,
            PLOT_MANHATTAN_THRESHOLD_DEFAULT);
    final Color background = config.getColor(PLOT_MANHATTAN_BACKGROUND_CONFIG,
            PLOT_MANHATTAN_BACKGROUND_DEFAULT);
    final Color backgroundAlternative = config.getColor(PLOT_MANHATTAN_BACKGROUND_ALTERNATIVE_CONFIG,
            PLOT_MANHATTAN_BACKGROUND_ALTERNATIVE_DEFAULT);
    final Color main = config.getColor(PLOT_MANHATTAN_MAIN_CONFIG, PLOT_MANHATTAN_MAIN_DEFAULT);

    Map<MarkerKey, MarkerManhattenData> markerKeyChrPosPVal = assembleManhattenPlotData(testOpKey);

    XYSeriesCollection currChrSC = new XYSeriesCollection();

    NumberAxis sharedAxis = new NumberAxis("-log?(P)");

    CombinedRangeXYPlot combinedPlot = new CombinedRangeXYPlot(sharedAxis);
    combinedPlot.setGap(0);/*from  w w w .  ja  v  a2 s .  c  o m*/

    XYSeries currChrS = null;

    // Subdividing points into sub-XYSeries, per chromosome
    String currChr = "";
    Map<String, MarkerKey> labeler = new LinkedHashMap<String, MarkerKey>(); // FIXME This is unused, was a global static var before (also private though), was the data added here actually used somewhere? (i think not)
    for (Map.Entry<MarkerKey, MarkerManhattenData> entry : markerKeyChrPosPVal.entrySet()) {
        MarkerKey markerKey = entry.getKey();
        MarkerManhattenData data = entry.getValue();

        if (data.getPValue() != null) {
            final double pVal = data.getPValue(); // Is allready free of NaN and infinity
            if (pVal < 1) {
                if (data.getChromosome().equals(currChr)) {
                    currChrS.add(data.getPosition(), pVal);
                    labeler.put(currChr + "_" + data.getPosition(), markerKey);
                } else {
                    if (!currChr.isEmpty()) { // SKIP FIRST TIME (NO DATA YET!)
                        // add the last (now compleeted) chromosomes data-set,
                        // before starting the new one
                        currChrSC.addSeries(currChrS);
                        appendToCombinedRangeManhattanPlot(combinedPlot, currChr, currChrSC, false, threshold,
                                background, backgroundAlternative, main);
                    }
                    currChr = data.getChromosome();
                    currChrSC = new XYSeriesCollection();
                    currChrS = new XYSeries(currChr);
                    labeler.put(currChr + "_" + data.getPosition(), markerKey);

                    currChrS.add(data.getPosition(), pVal);
                }
            }
        }
    }
    if (currChrS != null) {
        currChrSC.addSeries(currChrS);
        // ADD LAST CHR TO PLOT
        appendToCombinedRangeManhattanPlot(combinedPlot, currChr, currChrSC, true, threshold, background,
                backgroundAlternative, main);
    }

    // Remove Legend from the bottom of the chart
    combinedPlot.setFixedLegendItems(new LegendItemCollection());

    return combinedPlot;
}

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