List of usage examples for org.jfree.chart.axis LogAxis setAutoRangeMinimumSize
public void setAutoRangeMinimumSize(double size)
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);// ww w . j a v a 2 s. com 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:ecosim.gui.SummaryPane.java
/** * Private method to build the binning chart. * * @return A ChartPanel containing the binning chart. *///from w w w. ja v a 2 s .co m private ChartPanel makeBinningChart() { final DefaultXYDataset binData = new DefaultXYDataset(); final NumberFormat nf = NumberFormat.getInstance(); final NumberAxis xAxis = new NumberAxis("Sequence identity criterion"); nf.setMinimumFractionDigits(2); xAxis.setLowerBound(Binning.binLevels[0]); xAxis.setUpperBound(1.0D); xAxis.setTickUnit(new NumberTickUnit(0.05D, nf)); LogAxis yAxis = new LogAxis("Number of bins"); yAxis.setBase(2.0D); yAxis.setNumberFormatOverride(NumberFormat.getInstance()); yAxis.setTickUnit(new NumberTickUnit(2.0D)); yAxis.setMinorTickMarksVisible(true); yAxis.setAutoRangeMinimumSize(4.0D); yAxis.setSmallestValue(1.0D); XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(true, false); for (int i = 0; i < seriesColors.length; i++) { renderer.setSeriesPaint(i, seriesColors[i]); renderer.setSeriesStroke(i, new BasicStroke(seriesStroke[i])); } XYPlot plot = new XYPlot(binData, xAxis, yAxis, renderer); JFreeChart binChart = new JFreeChart(null, JFreeChart.DEFAULT_TITLE_FONT, plot, false); binChart.setPadding(new RectangleInsets(0.0D, 0.0D, 0.0D, 10.0D)); LegendTitle legend = new LegendTitle(plot); legend.setMargin(new RectangleInsets(1.0D, 1.0D, 1.0D, 1.0D)); legend.setFrame(new LineBorder()); legend.setBackgroundPaint(Color.white); legend.setPosition(RectangleEdge.BOTTOM); plot.addAnnotation(new XYTitleAnnotation(0.001D, 0.999D, legend, RectangleAnchor.TOP_LEFT)); final ChartPanel pane = new ChartPanel(binChart, false, true, true, false, false); // Watch for changes to the Summary object. summary.addObserver(new Observer() { public void update(Observable o, Object obj) { Summary s = (Summary) obj; ParameterEstimate estimate = s.getEstimate(); ArrayList<BinLevel> bins = s.getBins(); if (bins.size() > 0) { double[][] values = new double[2][bins.size()]; Double low = 1.0d; for (int i = 0; i < bins.size(); i++) { BinLevel bin = bins.get(i); values[0][i] = bin.getCrit(); values[1][i] = bin.getLevel(); if (values[0][i] < low) low = values[0][i]; } binData.addSeries("sequences", values); xAxis.setLowerBound(low); if (low > 0.95d - MasterVariables.EPSILON) { xAxis.setTickUnit(new NumberTickUnit(0.005D, nf)); } else if (low > 0.90d - MasterVariables.EPSILON) { xAxis.setTickUnit(new NumberTickUnit(0.010D, nf)); } else if (low > 0.80d - MasterVariables.EPSILON) { xAxis.setTickUnit(new NumberTickUnit(0.025D, nf)); } if (estimate != null) { double[][] omega = new double[2][bins.size()]; double[][] sigma = new double[2][bins.size()]; double[] omegaLine = estimate.getOmega(); double[] sigmaLine = estimate.getSigma(); for (int i = 0; i < bins.size(); i++) { double crit = 1.0D - values[0][i]; double snp = s.getLength() * crit; omega[0][i] = values[0][i]; sigma[0][i] = values[0][i]; omega[1][i] = Math.pow(2.0D, snp * omegaLine[0] + omegaLine[1]); sigma[1][i] = Math.pow(2.0D, snp * sigmaLine[0] + sigmaLine[1]); } if (-1.0D * omegaLine[0] > MasterVariables.EPSILON) { binData.addSeries("omega", omega); } if (-1.0D * sigmaLine[0] > MasterVariables.EPSILON) { binData.addSeries("sigma", sigma); } } // Repaint the summary pane. pane.repaint(); } } }); return pane; }