List of usage examples for org.jfree.chart.axis LogAxis setAxisLineVisible
public void setAxisLineVisible(boolean visible)
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 va 2 s.co 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);//www . j a va2 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); }
From source file:org.gwaspi.gui.reports.ManhattanPlotZoom.java
private JFreeChart createChart(XYDataset dataset, ChromosomeKey chr) { JFreeChart chart = ChartFactory.createScatterPlot(null, "", "P value", dataset, PlotOrientation.VERTICAL, true, false, false);/* w ww .j av a2 s. c o m*/ XYPlot plot = (XYPlot) chart.getPlot(); plot.setNoDataMessage("NO DATA"); plot.setDomainZeroBaselineVisible(true); plot.setRangeZeroBaselineVisible(true); // CHART BACKGROUD COLOR chart.setBackgroundPaint(Color.getHSBColor(0.1f, 0.1f, 1.0f)); // Hue, saturation, brightness plot.setBackgroundPaint(manhattan_back); // Hue, saturation, brightness 9 // GRIDLINES plot.setDomainGridlineStroke(new BasicStroke(0.0f)); plot.setDomainMinorGridlineStroke(new BasicStroke(0.0f)); plot.setDomainGridlinePaint(manhattan_back.darker().darker()); // Hue, saturation, brightness 7 plot.setDomainMinorGridlinePaint(manhattan_back); // Hue, saturation, brightness 9 plot.setRangeGridlineStroke(new BasicStroke(0.0f)); plot.setRangeMinorGridlineStroke(new BasicStroke(0.0f)); plot.setRangeGridlinePaint(manhattan_back.darker().darker()); // Hue, saturation, brightness 7 plot.setRangeMinorGridlinePaint(manhattan_back.darker()); // Hue, saturation, brightness 8 plot.setDomainMinorGridlinesVisible(true); plot.setRangeMinorGridlinesVisible(true); // DOTS RENDERER XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesPaint(0, manhattan_dot); // renderer.setSeriesOutlinePaint(0, Color.DARK_GRAY); // renderer.setUseOutlinePaint(true); // Set dot shape of the currently appended Series renderer.setSeriesShape(0, new Rectangle2D.Double(0.0, 0.0, 2, 2)); renderer.setSeriesVisibleInLegend(0, false); NumberAxis positionAxis = (NumberAxis) plot.getDomainAxis(); // domainAxis.setAutoRangeIncludesZero(false); // domainAxis.setTickMarkInsideLength(2.0f); // domainAxis.setTickMarkOutsideLength(2.0f); // domainAxis.setMinorTickCount(2); // domainAxis.setMinorTickMarksVisible(true); positionAxis.setLabelAngle(1.0); positionAxis.setAutoRangeIncludesZero(false); positionAxis.setAxisLineVisible(true); positionAxis.setTickLabelsVisible(true); positionAxis.setTickMarksVisible(true); // ADD INVERSE LOG(10) Y AXIS LogAxis logPAxis = new LogAxis("P value"); logPAxis.setBase(10); logPAxis.setInverted(true); logPAxis.setNumberFormatOverride(GenericReportGenerator.FORMAT_P_VALUE); logPAxis.setTickMarkOutsideLength(2.0f); logPAxis.setMinorTickCount(2); logPAxis.setMinorTickMarksVisible(true); logPAxis.setAxisLineVisible(true); logPAxis.setUpperMargin(0); TickUnitSource units = NumberAxis.createIntegerTickUnits(); logPAxis.setStandardTickUnits(units); plot.setRangeAxis(0, logPAxis); // Add significance Threshold to subplot //threshold = 0.5/rdMatrixMetadata.getMarkerSetSize(); // (0.05/10? SNPs => 5*10-?) final Marker thresholdLine = new ValueMarker(threshold); thresholdLine.setPaint(Color.red); // Add legend to threshold thresholdLine.setLabel("P = " + GenericReportGenerator.FORMAT_P_VALUE.format(threshold)); thresholdLine.setLabelAnchor(RectangleAnchor.TOP_RIGHT); thresholdLine.setLabelTextAnchor(TextAnchor.BOTTOM_RIGHT); plot.addRangeMarker(thresholdLine); // Marker label if below threshold XYItemRenderer lblRenderer = plot.getRenderer(); // THRESHOLD AND SELECTED LABEL GENERATOR MySeriesItemLabelGenerator lblGenerator = new MySeriesItemLabelGenerator(threshold, chr); lblRenderer.setSeriesItemLabelGenerator(0, lblGenerator); lblRenderer.setSeriesItemLabelFont(0, new Font("SansSerif", Font.PLAIN, 12)); lblRenderer.setSeriesPositiveItemLabelPosition(0, new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.TOP_LEFT, TextAnchor.BOTTOM_LEFT, Math.PI / 4.0)); // TOOLTIP GENERATOR MyXYToolTipGenerator tooltipGenerator = new MyXYToolTipGenerator(chr); lblRenderer.setBaseToolTipGenerator(tooltipGenerator); lblRenderer.setSeriesItemLabelsVisible(0, true); return chart; }