List of usage examples for org.jfree.chart.axis LogAxis setNumberFormatOverride
public void setNumberFormatOverride(NumberFormat formatter)
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);/* w w w . ja va 2 s .c om*/ 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);/*ww w . j a va 2s . 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:netplot.GenericPlotPanel.java
void genericConfig(JFreeChart chart, XYPlot plot, int plotIndex) { if (!enableLegend) { chart.removeLegend();//from w w w . j a v a 2s .c om } XYItemRenderer xyItemRenderer = plot.getRenderer(); //May also be XYBarRenderer if (xyItemRenderer instanceof XYLineAndShapeRenderer) { XYToolTipGenerator xyToolTipGenerator = xyItemRenderer.getBaseToolTipGenerator(); //If currently an XYLineAndShapeRenderer replace it so that we inc the colour for every plotIndex XYLineAndShapeRenderer renderer = new XYLineAndShapeRenderer(linesEnabled, shapesEnabled); //Ensure we don't loose the tool tips on the new renderer renderer.setBaseToolTipGenerator(xyToolTipGenerator); renderer.setBasePaint(getPlotColour(plotIndex)); renderer.setSeriesStroke(0, new BasicStroke(lineWidth, BasicStroke.CAP_BUTT, BasicStroke.JOIN_BEVEL), true); plot.setRenderer(plotIndex, renderer); } //If we have a new y axis then we need a new data set if (yAxisName != null && yAxisName.length() > 0) { if (logYAxis) { LogAxis yAxis = new LogAxis(yAxisName); yAxis.setAutoRange(false); yAxis.setNumberFormatOverride(new LogFormat(10, "10", true)); yAxis.setRange(minScaleValue, maxScaleValue); yAxis.setLowerBound(minScaleValue); yAxis.setUpperBound(maxScaleValue); plot.setRangeAxis(yAxisIndex, yAxis); plot.setRangeAxisLocation(yAxisIndex, AxisLocation.BOTTOM_OR_LEFT); } else { NumberAxis axis = new NumberAxis(yAxisName); axis.setAutoRangeIncludesZero(zeroOnYScale); if (autoScaleEnabled) { axis.setAutoRange(true); } else { Range range = new Range(minScaleValue, maxScaleValue); axis.setRangeWithMargins(range, true, true); } if (yAxisTickCount > 0) { NumberTickUnit tick = new NumberTickUnit(yAxisTickCount); axis.setTickUnit(tick); } plot.setRangeAxis(yAxisIndex, axis); plot.setRangeAxisLocation(yAxisIndex, AxisLocation.BOTTOM_OR_LEFT); } yAxisIndex++; } plot.mapDatasetToRangeAxis(plotIndex, yAxisIndex - 1); ValueAxis a = plot.getDomainAxis(); if (xAxisName.length() > 0) { a.setLabel(xAxisName); } //We can enable/disable zero on the axis if we have a NumberAxis if (a instanceof NumberAxis) { ((NumberAxis) a).setAutoRangeIncludesZero(zeroOnXScale); } }
From source file:net.sf.mzmine.modules.visualization.scatterplot.scatterplotchart.ScatterPlotChart.java
public ScatterPlotChart(ScatterPlotTopPanel topPanel, PeakList peakList) { super(null, true); this.peakList = peakList; this.topPanel = topPanel; // initialize the chart by default time series chart from factory chart = ChartFactory.createXYLineChart("", // title "", // x-axis label "", // y-axis label null, // data set PlotOrientation.VERTICAL, // orientation false, // create legend false, // generate tooltips false // generate URLs );//from w ww.j a v a2 s . com chart.setBackgroundPaint(Color.white); setChart(chart); // disable maximum size (we don't want scaling) setMaximumDrawWidth(Integer.MAX_VALUE); setMaximumDrawHeight(Integer.MAX_VALUE); // set the plot properties plot = chart.getXYPlot(); plot.setBackgroundPaint(Color.white); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD); plot.setDomainGridlinePaint(gridColor); plot.setRangeGridlinePaint(gridColor); // Set the domain log axis LogAxis logAxisDomain = new LogAxis(); logAxisDomain.setMinorTickCount(1); logAxisDomain.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat()); logAxisDomain.setAutoRange(true); plot.setDomainAxis(logAxisDomain); // Set the range log axis LogAxis logAxisRange = new LogAxis(); logAxisRange.setMinorTickCount(1); logAxisRange.setNumberFormatOverride(MZmineCore.getConfiguration().getIntensityFormat()); logAxisRange.setAutoRange(true); plot.setRangeAxis(logAxisRange); // Set crosshair properties plot.setDomainCrosshairVisible(true); plot.setRangeCrosshairVisible(true); plot.setDomainCrosshairPaint(crossHairColor); plot.setRangeCrosshairPaint(crossHairColor); plot.setDomainCrosshairStroke(crossHairStroke); plot.setRangeCrosshairStroke(crossHairStroke); // Create data sets; mainDataSet = new ScatterPlotDataSet(peakList); plot.setDataset(0, mainDataSet); diagonalLineDataset = new DiagonalLineDataset(); plot.setDataset(1, diagonalLineDataset); // Create renderers mainRenderer = new ScatterPlotRenderer(); plot.setRenderer(0, mainRenderer); diagonalLineRenderer = new DiagonalLineRenderer(); plot.setRenderer(1, diagonalLineRenderer); // Set tooltip properties ttm = new ComponentToolTipManager(); ttm.registerComponent(this); setDismissDelay(Integer.MAX_VALUE); setInitialDelay(0); // add items to popup menu TODO: add other Show... items JPopupMenu popupMenu = getPopupMenu(); popupMenu.addSeparator(); GUIUtils.addMenuItem(popupMenu, "Show Chromatogram", this, "TIC"); }
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. j av a2 s . c om 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; }
From source file:com.wattzap.view.graphs.MMPGraph.java
public MMPGraph(XYSeries series) { super();/*from w w w .jav a 2 s. com*/ NumberAxis yAxis = new NumberAxis(userPrefs.messages.getString("poWtt")); yAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); double maxY = series.getMaxY(); yAxis.setRange(0, maxY + 20); yAxis.setTickLabelPaint(Color.white); yAxis.setLabelPaint(Color.white); LogAxis xAxis = new LogAxis(userPrefs.messages.getString("time")); xAxis.setTickLabelPaint(Color.white); xAxis.setBase(4); xAxis.setAutoRange(false); xAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); xAxis.setRange(1, series.getMaxX() + 500); xAxis.setNumberFormatOverride(new NumberFormat() { @Override public StringBuffer format(double number, StringBuffer toAppendTo, FieldPosition pos) { long millis = (long) number * 1000; if (millis >= 60000) { return new StringBuffer(String.format("%d m %d s", TimeUnit.MILLISECONDS.toMinutes((long) millis), TimeUnit.MILLISECONDS.toSeconds((long) millis) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes((long) millis)))); } else { return new StringBuffer(String.format("%d s", TimeUnit.MILLISECONDS.toSeconds((long) millis) - TimeUnit.MINUTES.toSeconds(TimeUnit.MILLISECONDS.toMinutes((long) millis)))); } } @Override public StringBuffer format(long number, StringBuffer toAppendTo, FieldPosition pos) { return new StringBuffer(String.format("%s", number)); } @Override public Number parse(String source, ParsePosition parsePosition) { return null; } }); XYPlot plot = new XYPlot(new XYSeriesCollection(series), xAxis, yAxis, new XYLineAndShapeRenderer(true, false)); JFreeChart chart = new JFreeChart("", JFreeChart.DEFAULT_TITLE_FONT, plot, false); chart.setBackgroundPaint(Color.gray); plot = chart.getXYPlot(); plot.setBackgroundPaint(Color.darkGray); /*plot.setDomainGridlinePaint(Color.lightGray); plot.setRangeGridlinePaint(Color.lightGray);*/ ValueAxis domainAxis = plot.getDomainAxis(); domainAxis.setTickLabelPaint(Color.white); domainAxis.setLabelPaint(Color.white); chartPanel = new ChartPanel(chart); chartPanel.setSize(100, 800); chartPanel.setFillZoomRectangle(true); chartPanel.setMouseWheelEnabled(true); chartPanel.setBackground(Color.gray); setLayout(new BorderLayout()); add(chartPanel, BorderLayout.CENTER); setBackground(Color.black); chartPanel.revalidate(); setVisible(true); }
From source file:org.pf.midea.SimulationController.java
@Override public void run() { textAreaNumeric.setText(""); XYSeriesCollection xySeriesCollection = new XYSeriesCollection(); double progress = 0; double progressStep = 100.0 / (planCells.length * (hSquareHigh - hSquareLow + hSquareStep) / hSquareStep); progressBar.setValue(0);//from w w w . j av a 2 s .c om for (int i = 0; i < planCells.length; i++) { XYSeries xySeries; if (showLineNumbers) xySeries = new XYSeries(String.valueOf(i + 1) + ") " + planCells[i].getShortDescription()); else xySeries = new XYSeries(planCells[i].getShortDescription()); textAreaNumeric.append(planCells[i].getDescription() + "\n"); textAreaNumeric.setCaretPosition(textAreaNumeric.getDocument().getLength()); PlanStates.SourceType currentSourceType = planCells[i].getSourceCell().getSourceType(); PlanStates.CodeType currentCodeType = planCells[i].getCodeCell().getCodeType(); PlanStates.ModulationType currentModulationType = planCells[i].getModulationCell().getModulationType(); PlanStates.ChannelType currentChannelType = planCells[i].getChannelCell().getChannelType(); PlanStates.ErrorsType currentErrorsType = planCells[i].getErrorsCell().getErrorsType(); BinaryNumber[] sourcePoints = null; switch (currentSourceType) { case ST_TEST: sourcePoints = ConstellationPointsGenerator.getTestPoints(currentModulationType, iterationsCount); break; case ST_RANDOM: sourcePoints = ConstellationPointsGenerator.getRandomPoints(currentModulationType, iterationsCount); break; } Coder coder = null; Decoder decoder = null; switch (currentCodeType) { case CT_NONE: coder = new CoderNone(); decoder = new DecoderNone(); break; case CT_HAMMING74: coder = new CoderHamming74(); decoder = new DecoderHamming74(); break; case CT_CYCLIC: coder = new CoderCyclic85(); decoder = new DecoderCyclic85(); break; case CT_BCH155: coder = new CoderBCH155(); decoder = new DecoderBCH155(); break; } Modulator modulator = null; Demodulator demodulator = null; switch (currentModulationType) { case MT_ASK: modulator = new ModulatorASK(); demodulator = new DemodulatorASK(); break; case MT_FSK: modulator = new ModulatorFSK(); demodulator = new DemodulatorFSK(); break; case MT_BPSK: modulator = new ModulatorBPSK(); demodulator = new DemodulatorBPSK(); break; case MT_QPSK: modulator = new ModulatorQPSK(); demodulator = new DemodulatorQPSK(); break; case MT_8PSK: modulator = new Modulator8PSK(); demodulator = new Demodulator8PSK(); break; case MT_16PSK: modulator = new Modulator16PSK(); demodulator = new Demodulator16PSK(); break; case MT_32PSK: modulator = new Modulator32PSK(); demodulator = new Demodulator32PSK(); break; case MT_16QAM: modulator = new Modulator16QAM(); demodulator = new Demodulator16QAM(); break; case MT_32QAM: modulator = new Modulator32QAM(); demodulator = new Demodulator32QAM(); break; case MT_64QAM: modulator = new Modulator64QAM(); demodulator = new Demodulator64QAM(); break; case MT_256QAM: modulator = new Modulator256QAM(); demodulator = new Demodulator256QAM(); break; } Channel channel = null; switch (currentChannelType) { case CHT_AWGN: channel = new ChannelAWGN(); break; case CHT_RAYLEIGH: channel = new ChannelRayleigh(); break; } BinaryNumber[] encoded = coder.encode(sourcePoints); Signal[] modulated = modulator.modulate(encoded); double error = 0; for (double h = hSquareLow; h <= hSquareHigh; h += hSquareStep) { double realH; if (dBs) realH = StatisticsTools.decibelsToTimes(h); else realH = h; Signal[] noised = channel.noise(realH, modulated); BinaryNumber[] demodulated = demodulator.demodulate(noised); noised = null; System.gc(); BinaryNumber[] decoded = decoder.decode(demodulated); demodulated = null; System.gc(); switch (currentErrorsType) { case ET_SER: error = StatisticsTools.getSER(sourcePoints, decoded); break; case ET_BER: error = StatisticsTools.getBER(sourcePoints, decoded); break; } decoded = null; System.gc(); if (error > 0) { xySeries.add(h, error); textAreaNumeric.append(String.valueOf(h) + "\t" + String.valueOf(error) + "\n"); textAreaNumeric.setCaretPosition(textAreaNumeric.getDocument().getLength()); } progress += progressStep; progressBar.setValue((int) Math.round(progress)); } xySeriesCollection.addSeries(xySeries); textAreaNumeric.append("\n"); textAreaNumeric.setCaretPosition(textAreaNumeric.getDocument().getLength()); } JFreeChart chart = ChartFactory.createXYLineChart("", dBs ? "" : "", "?", xySeriesCollection, PlotOrientation.VERTICAL, true, true, false); chart.getLegend().setPosition(RectangleEdge.RIGHT); XYPlot xyPlot = chart.getXYPlot(); for (int i = 0; i < planCells.length; i++) { xyPlot.getRenderer().setSeriesStroke(i, new BasicStroke(planCells[i].getLineWidth())); if (planCells[i].getLineColor() != null) xyPlot.getRenderer().setSeriesPaint(i, planCells[i].getLineColor()); if (showLineNumbers) { XYSeries currentSeries = xySeriesCollection.getSeries(i); double annotationY = currentSeries.getY(0).doubleValue(); double annotationX = currentSeries.getX(0).doubleValue(); for (int j = 1; j < currentSeries.getItemCount(); j++) if (currentSeries.getY(j).doubleValue() == 0) { annotationY = currentSeries.getY(j - 1).doubleValue(); annotationX = currentSeries.getX(j - 1).doubleValue(); break; } else { annotationY = currentSeries.getY(j).doubleValue(); annotationX = currentSeries.getX(j).doubleValue(); } XYTextAnnotation annotation = new XYTextAnnotation(String.valueOf(i + 1), annotationX, annotationY); annotation.setBackgroundPaint(Color.WHITE); annotation.setFont(new Font("Dialog", 0, 14)); xyPlot.addAnnotation(annotation); } } xyPlot.setBackgroundPaint(Color.WHITE); xyPlot.setDomainGridlinePaint(Color.GRAY); xyPlot.setRangeGridlinePaint(Color.GRAY); NumberAxis domainAxis = new NumberAxis("h, " + (dBs ? "" : "")); LogAxis rangeAxis = new LogAxis("?"); rangeAxis.setNumberFormatOverride(new HumanNumberFormat(1)); domainAxis.setTickLabelFont(new Font("Dialog", 0, 14)); rangeAxis.setTickLabelFont(new Font("Dialog", 0, 14)); xyPlot.setDomainAxis(domainAxis); xyPlot.setRangeAxis(rangeAxis); ChartPanel nestedPanel = new ChartPanel(chart); chartPanel.removeAll(); chartPanel.add(nestedPanel, new CellConstraints()); chartPanel.updateUI(); }
From source file:edu.fullerton.viewerplugin.XYPlotter.java
private ChartPanel getPanel(double[][] data) throws WebUtilException { ChartPanel ret = null;/*from ww w . jav a2 s . c om*/ try { XYSeries xys; XYSeriesCollection mtds = new XYSeriesCollection(); String mylegend = legend == null || legend.isEmpty() ? "series 1" : legend; xys = new XYSeries(legend); int len = data.length; double minx = Double.MAX_VALUE; double maxx = Double.MIN_VALUE; double miny = Double.MAX_VALUE; double maxy = Double.MIN_VALUE; boolean gotZeroX = false; boolean gotZeroY = false; for (int i = 0; i < len; i++) { double x = data[i][0]; double y = data[i][1]; if (x == 0) { gotZeroX = true; } else { minx = Math.min(minx, x); maxx = Math.max(maxx, x); } if (y == 0) { gotZeroY = true; } else { miny = Math.min(miny, y); maxy = Math.max(maxy, y); } } // this kludge lets us plot a 0 on a log axis double fakeZeroX = 0.; double fakeZeroY = 0.; if (gotZeroX) { if (logXaxis) { fakeZeroX = minx / 10; } else { minx = Math.min(0, minx); maxx = Math.max(0, maxx); } } if (gotZeroY) { if (logYaxis) { fakeZeroY = miny / 10; } else { miny = Math.min(0, miny); maxy = Math.max(0, maxy); } } for (int i = 0; i < len; i++) { double x = data[i][0]; double y = data[i][1]; x = x == 0 ? fakeZeroX : x; y = y == 0 ? fakeZeroY : y; xys.add(x, y); } mtds.addSeries(xys); DefaultXYDataset ds = new DefaultXYDataset(); int exp; if (maxy == 0. && miny == 0.) { miny = -1.; exp = 0; logYaxis = false; } else { maxy = maxy > miny ? maxy : miny * 10; exp = PluginSupport.scaleRange(mtds, miny, maxy); if (!logYaxis && exp > 0) { yLabel += " x 1e-" + Integer.toString(exp); } } JFreeChart chart = ChartFactory.createXYLineChart(title, xLabel, yLabel, ds, PlotOrientation.VERTICAL, true, false, false); org.jfree.chart.plot.XYPlot plot = (org.jfree.chart.plot.XYPlot) chart.getPlot(); if (logYaxis) { LogAxis rangeAxis = new LogAxis(yLabel); double smallest = miny * Math.pow(10, exp); rangeAxis.setSmallestValue(smallest); rangeAxis.setMinorTickCount(9); LogAxisNumberFormat lanf = new LogAxisNumberFormat(); lanf.setExp(exp); rangeAxis.setNumberFormatOverride(lanf); rangeAxis.setRange(smallest, maxy * Math.pow(10, exp)); plot.setRangeAxis(rangeAxis); } if (logXaxis) { LogAxis domainAxis = new LogAxis(xLabel); domainAxis.setMinorTickCount(9); domainAxis.setSmallestValue(minx); domainAxis.setNumberFormatOverride(new LogAxisNumberFormat()); plot.setDomainAxis(domainAxis); } ValueAxis domainAxis = plot.getDomainAxis(); if (fmin != null && fmin > 0) { domainAxis.setLowerBound(fmin); } if (fmax != null && fmax > 0) { domainAxis.setUpperBound(fmax); } plot.setDomainAxis(domainAxis); plot.setDataset(0, mtds); // Set the line thickness XYLineAndShapeRenderer r = (XYLineAndShapeRenderer) plot.getRenderer(); BasicStroke str = new BasicStroke(lineThickness); int n = plot.getSeriesCount(); for (int i = 0; i < n; i++) { r.setSeriesStroke(i, str); } if (legend == null || legend.isEmpty()) { chart.removeLegend(); } ret = new ChartPanel(chart); } catch (Exception ex) { throw new WebUtilException("Creating spectrum plot" + ex.getLocalizedMessage()); } return ret; }
From source file:eu.planets_project.tb.impl.chart.ExperimentChartServlet.java
public JFreeChart createXYChart(String expId) { ExperimentPersistencyRemote edao = ExperimentPersistencyImpl.getInstance(); long eid = Long.parseLong(expId); log.info("Building experiment chart for eid = " + eid); Experiment exp = edao.findExperiment(eid); final String expName = exp.getExperimentSetup().getBasicProperties().getExperimentName(); final XYSeries series = new XYSeries(expName); for (BatchExecutionRecordImpl batch : exp.getExperimentExecutable().getBatchExecutionRecords()) { int i = 1; for (ExecutionRecordImpl exr : batch.getRuns()) { //log.info("Found Record... "+exr+" stages: "+exr.getStages()); if (exr != null && exr.getStages() != null) { // Look up the object, so we can get the name. DigitalObjectRefBean dh = new DataHandlerImpl().get(exr.getDigitalObjectReferenceCopy()); String dobName = "Object " + i; if (dh != null) dobName = dh.getName(); for (ExecutionStageRecordImpl exsr : exr.getStages()) { Double time = exsr.getDoubleMeasurement(TecRegMockup.PROP_SERVICE_TIME); Double size = exsr.getDoubleMeasurement(TecRegMockup.PROP_DO_SIZE); // Look for timing: if (time != null && size != null && size.doubleValue() > 0.0 && time.doubleValue() > 0.0) { series.add(size, time); /* if( exsr.isMarkedAsSuccessful() ) { dataset.addValue( time, "Succeded", dobName); } else {// www . ja v a2 s .com dataset.addValue( time, "Failed", dobName); } */ } } } // Increment, for the next run. i++; } } // Create the chart. JFreeChart chart = ChartFactory.createScatterPlot(null, "Size [bytes]", "Time [s]", new XYSeriesCollection(series), PlotOrientation.VERTICAL, true, true, false); XYPlot plot = (XYPlot) chart.getPlot(); LogAxis xAxis = new LogAxis("Size [bytes]"); // Set the base appropriately: xAxis.setBase(1024.0); // xAxis.setTickUnit( new NumberTickUnit(128.0) ); // xAxis.getTickUnit().getMinorTickCount(); // FIXME This should really be a KB/MB/etc number formatter... xAxis.setNumberFormatOverride(new LogFormat(1024.0, "1024", true)); // LogAxis yAxis = new LogAxis("Y"); // yAxis.setNumberFormatOverride(new LogFormat(10.0, "10", true)); plot.setDomainAxis(xAxis); // plot.setRangeAxis(yAxis); // Add some tool-tips plot.getRenderer().setBaseToolTipGenerator(new StandardXYToolTipGenerator()); return chart; }
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);//from w ww . j ava 2 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; }