List of usage examples for org.jfree.chart.axis CategoryAxis setCategoryLabelPositions
public void setCategoryLabelPositions(CategoryLabelPositions positions)
From source file:mzmatch.ipeak.normalisation.VanDeSompele.java
public static void main(String args[]) { try {/*from w ww. j a va2 s .c o m*/ Tool.init(); // parse the commandline options Options options = new Options(); CmdLineParser cmdline = new CmdLineParser(options); // check whether we need to show the help cmdline.parse(args); if (options.help) { Tool.printHeader(System.out, application, version); cmdline.printUsage(System.out, ""); return; } if (options.verbose) { Tool.printHeader(System.out, application, version); cmdline.printOptions(); } // check the command-line parameters { // if the output directories do not exist, create them if (options.output != null) Tool.createFilePath(options.output, true); } // load the data if (options.verbose) System.out.println("Loading data"); ParseResult result = PeakMLParser.parse(new FileInputStream(options.input), true); Header header = result.header; IPeakSet<IPeakSet<? extends IPeak>> peaksets = (IPeakSet<IPeakSet<? extends IPeak>>) result.measurement; int nrmeasurements = header.getNrMeasurementInfos(); // remove the stability factor annotation for (IPeak peak : peaksets) peak.removeAnnotation("stability factor"); // load the database if (options.verbose) System.out.println("Loading the molecule database"); HashMap<String, Molecule> database = MoleculeIO.parseXml(new FileInputStream(options.database)); // filter the set to include only identifiable metabolites if (options.verbose) System.out.println("Creating selection"); Vector<IPeakSet<? extends IPeak>> selection = new Vector<IPeakSet<? extends IPeak>>(); for (Molecule molecule : database.values()) { double mass = molecule.getMass(Mass.MONOISOTOPIC); double delta = PeriodicTable.PPM(mass, options.ppm); // get the most intense peak containing all the measurements Vector<IPeakSet<? extends IPeak>> neighbourhoud = peaksets.getPeaksInMassRange(mass - delta, mass + delta); Collections.sort(neighbourhoud, IPeak.sort_intensity_descending); for (IPeakSet<? extends IPeak> neighbour : neighbourhoud) if (count(neighbour) == nrmeasurements) { selection.add(neighbour); break; } } // calculate the stability factor for each peak in the selection if (options.verbose) System.out.println("Calculating stability factors"); for (int peakid1 = 0; peakid1 < selection.size(); ++peakid1) { double stddeviations[] = new double[selection.size()]; IPeakSet<? extends IPeak> peakset1 = selection.get(peakid1); for (int peakid2 = 0; peakid2 < selection.size(); ++peakid2) { IPeakSet<? extends IPeak> peakset2 = selection.get(peakid2); double values[] = new double[nrmeasurements]; for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { int measurementid1 = peakset1.get(measurementid).getMeasurementID(); int setid1 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid1)); int measurementid2 = peakset2.get(measurementid).getMeasurementID(); int setid2 = header.indexOfSetInfo(header.getSetInfoForMeasurementID(measurementid2)); if (setid1 != setid2 || measurementid1 != measurementid2) System.err.println("[WARNING]: differing setid or spectrumid for comparison"); values[measurementid] = Math.log(peakset1.get(measurementid).getIntensity() / peakset2.get(measurementid).getIntensity()) / Math.log(2); } stddeviations[peakid2] = Statistical.stddev(values); } peakset1.addAnnotation("stability factor", Statistical.mean(stddeviations)); } // sort on the stability factor Collections.sort(selection, new IPeak.AnnotationAscending("stability factor")); // take the top 10% and calculate the geometric mean if (options.verbose) System.out.println("Calculating normalisation factors"); int nrselected = (int) (0.1 * selection.size()); if (nrselected < 10) nrselected = (10 < selection.size() ? 10 : selection.size()); double normalization_factors[] = new double[nrmeasurements]; for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { double values[] = new double[nrselected]; for (int i = 0; i < nrselected; ++i) { IPeak peak = selection.get(i).get(measurementid); values[i] = peak.getIntensity(); } normalization_factors[measurementid] = Statistical.geomean(values); } // scale the found normalization factors double maxnf = Statistical.max(normalization_factors); for (int sampleid = 0; sampleid < nrmeasurements; ++sampleid) normalization_factors[sampleid] /= maxnf; // write the selection if needed if (options.selection != null) { if (options.verbose) System.out.println("Writing original selection data"); PeakMLWriter.write(result.header, selection, null, new GZIPOutputStream(new FileOutputStream(options.selection)), null); } // normalize all the peaks if (options.verbose) System.out.println("Normalizing all the entries"); for (IPeakSet<? extends IPeak> peakset : peaksets) { for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) { // TODO why did I do this again ? int id = 0; int setid = 0; int spectrumid = 0; for (int i = 0; i < header.getNrSetInfos(); ++i) { SetInfo set = header.getSetInfos().get(i); if (id + set.getNrMeasurementIDs() > measurementid) { setid = i; spectrumid = measurementid - id; break; } else id += set.getNrMeasurementIDs(); } MassChromatogram<Peak> masschromatogram = null; for (IPeak p : peakset) { int mymeasurementid = p.getMeasurementID(); int mysetid = header.indexOfSetInfo(header.getSetInfoForMeasurementID(mymeasurementid)); if (mysetid == setid && mymeasurementid == spectrumid) { masschromatogram = (MassChromatogram<Peak>) p; break; } } if (masschromatogram == null) continue; for (IPeak peak : masschromatogram.getPeaks()) peak.setIntensity(peak.getIntensity() / normalization_factors[measurementid]); } } // write the selection if needed if (options.selection_normalized != null) { if (options.verbose) System.out.println("Writing the normalized selection data"); PeakMLWriter.write(result.header, selection, null, new GZIPOutputStream(new FileOutputStream(options.selection_normalized)), null); } // write the factors if needed if (options.factors != null) { if (options.verbose) System.out.println("Writing the normalization factors"); PrintStream out = new PrintStream(options.factors); for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) out.println(header.getMeasurementInfo(measurementid).getLabel() + "\t" + normalization_factors[measurementid]); } // write the plot if needed if (options.img != null) { if (options.verbose) System.out.println("Writing the graph"); DefaultCategoryDataset dataset = new DefaultCategoryDataset(); JFreeChart linechart = ChartFactory.createLineChart(null, "measurement", "normalization factor", dataset, PlotOrientation.VERTICAL, false, // legend false, // tooltips false // urls ); CategoryPlot plot = (CategoryPlot) linechart.getPlot(); CategoryAxis axis = (CategoryAxis) plot.getDomainAxis(); axis.setCategoryLabelPositions(CategoryLabelPositions.UP_45); LineAndShapeRenderer renderer = (LineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesShapesFilled(0, true); renderer.setSeriesShapesVisible(0, true); linechart.setBackgroundPaint(Color.WHITE); linechart.setBorderVisible(false); linechart.setAntiAlias(true); plot.setBackgroundPaint(Color.WHITE); plot.setDomainGridlinesVisible(true); plot.setRangeGridlinesVisible(true); // create the datasets for (int measurementid = 0; measurementid < nrmeasurements; ++measurementid) dataset.addValue(normalization_factors[measurementid], "", header.getMeasurementInfo(measurementid).getLabel()); JFreeChartTools.writeAsPDF(new FileOutputStream(options.img), linechart, 800, 500); } // write the normalized values if (options.verbose) System.out.println("Writing the normalized data"); PeakMLWriter.write(result.header, peaksets.getPeaks(), null, new GZIPOutputStream(new FileOutputStream(options.output)), null); } catch (Exception e) { Tool.unexpectedError(e, application); } }
From source file:org.jfree.chart.demo.BarChartDemo10.java
private static JFreeChart createChart(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Bar Chart Demo", "Category", "Value", categorydataset, PlotOrientation.VERTICAL, true, true, false); jfreechart.setBackgroundPaint(Color.white); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setBackgroundPaint(Color.lightGray); categoryplot.setDomainGridlinePaint(Color.white); categoryplot.setDomainGridlinesVisible(true); categoryplot.setRangeGridlinePaint(Color.white); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); barrenderer.setSeriesPaint(0, gradientpaint); barrenderer.setSeriesPaint(1, gradientpaint1); barrenderer.setSeriesPaint(2, gradientpaint2); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions( CategoryLabelPositions.createUpRotationLabelPositions(0.52359877559829882D)); return jfreechart; }
From source file:org.jfree.chart.demo.AreaChartDemo1.java
private static JFreeChart createChart(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createAreaChart("Area Chart", "Category", "Value", categorydataset, PlotOrientation.VERTICAL, true, true, false); jfreechart.setBackgroundPaint(Color.white); TextTitle texttitle = new TextTitle( "An area chart demonstration. We use this subtitle as an example of what happens when you get a really long title or subtitle."); texttitle.setFont(new Font("SansSerif", 0, 12)); texttitle.setPosition(RectangleEdge.TOP); texttitle.setPadding(new RectangleInsets(UnitType.RELATIVE, 0.050000000000000003D, 0.050000000000000003D, 0.050000000000000003D, 0.050000000000000003D)); texttitle.setVerticalAlignment(VerticalAlignment.BOTTOM); jfreechart.addSubtitle(texttitle);//from w w w.j a va2 s . co m CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setForegroundAlpha(0.5F); categoryplot.setAxisOffset(new RectangleInsets(5D, 5D, 5D, 5D)); categoryplot.setBackgroundPaint(Color.lightGray); categoryplot.setDomainGridlinesVisible(true); categoryplot.setDomainGridlinePaint(Color.white); categoryplot.setRangeGridlinesVisible(true); categoryplot.setRangeGridlinePaint(Color.white); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45); categoryaxis.setLowerMargin(0.0D); categoryaxis.setUpperMargin(0.0D); categoryaxis.addCategoryLabelToolTip("Type 1", "The first type."); categoryaxis.addCategoryLabelToolTip("Type 2", "The second type."); categoryaxis.addCategoryLabelToolTip("Type 3", "The third type."); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); numberaxis.setLabelAngle(0.0D); return jfreechart; }
From source file:org.jfree.chart.demo.DualAxisDemo1.java
private static JFreeChart createChart() { JFreeChart jfreechart = ChartFactory.createBarChart("Dual Axis Chart", "Category", "Value", createDataset1(), PlotOrientation.VERTICAL, false, true, false); jfreechart.setBackgroundPaint(Color.white); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setBackgroundPaint(new Color(238, 238, 255)); categoryplot.setDomainAxisLocation(AxisLocation.BOTTOM_OR_RIGHT); CategoryDataset categorydataset = createDataset2(); categoryplot.setDataset(1, categorydataset); categoryplot.mapDatasetToRangeAxis(1, 1); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions(CategoryLabelPositions.DOWN_45); NumberAxis numberaxis = new NumberAxis("Secondary"); categoryplot.setRangeAxis(1, numberaxis); LineAndShapeRenderer lineandshaperenderer = new LineAndShapeRenderer(); lineandshaperenderer.setBaseToolTipGenerator(new StandardCategoryToolTipGenerator()); categoryplot.setRenderer(1, lineandshaperenderer); categoryplot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); LegendTitle legendtitle = new LegendTitle(categoryplot.getRenderer(0)); legendtitle.setMargin(new RectangleInsets(2D, 2D, 2D, 2D)); legendtitle.setFrame(new BlockBorder()); LegendTitle legendtitle1 = new LegendTitle(categoryplot.getRenderer(1)); legendtitle1.setMargin(new RectangleInsets(2D, 2D, 2D, 2D)); legendtitle1.setFrame(new BlockBorder()); BlockContainer blockcontainer = new BlockContainer(new BorderArrangement()); blockcontainer.add(legendtitle, RectangleEdge.LEFT); blockcontainer.add(legendtitle1, RectangleEdge.RIGHT); blockcontainer.add(new EmptyBlock(2000D, 0.0D)); CompositeTitle compositetitle = new CompositeTitle(blockcontainer); compositetitle.setPosition(RectangleEdge.BOTTOM); jfreechart.addSubtitle(compositetitle); return jfreechart; }
From source file:userInterface.ManufactureRole.DecisionChartJPanel.java
private static JFreeChart createChart1(CategoryDataset categorydataset) { JFreeChart jfreechart = ChartFactory.createBarChart("Vaccine Sales", "Vaccine", "quantity", categorydataset, PlotOrientation.VERTICAL, true, true, false); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setDomainGridlinesVisible(true); categoryplot.setRangeCrosshairVisible(true); categoryplot.setRangeCrosshairPaint(Color.blue); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); BarRenderer barrenderer = (BarRenderer) categoryplot.getRenderer(); barrenderer.setDrawBarOutline(false); GradientPaint gradientpaint = new GradientPaint(0.0F, 0.0F, Color.blue, 0.0F, 0.0F, new Color(0, 0, 64)); GradientPaint gradientpaint1 = new GradientPaint(0.0F, 0.0F, Color.green, 0.0F, 0.0F, new Color(0, 64, 0)); GradientPaint gradientpaint2 = new GradientPaint(0.0F, 0.0F, Color.red, 0.0F, 0.0F, new Color(64, 0, 0)); barrenderer.setSeriesPaint(0, gradientpaint); barrenderer.setSeriesPaint(1, gradientpaint1); barrenderer.setSeriesPaint(2, gradientpaint2); barrenderer.setLegendItemToolTipGenerator(new StandardCategorySeriesLabelGenerator("Tooltip: {0}")); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setCategoryLabelPositions( CategoryLabelPositions.createUpRotationLabelPositions(0.52359877559829882D)); return jfreechart; }
From source file:org.jfree.chart.swt.demo.SWTBarChartDemo1.java
/** * Creates a sample chart./* www .j av a 2 s . c om*/ * * @param dataset the dataset. * * @return The chart. */ private static JFreeChart createChart(CategoryDataset dataset) { // create the chart... JFreeChart chart = ChartFactory.createBarChart("SWTBarChartDemo1", // chart title "Category", // domain axis label "Value", // range axis label dataset); // NOW DO SOME OPTIONAL CUSTOMISATION OF THE CHART... // get a reference to the plot for further customisation... CategoryPlot plot = (CategoryPlot) chart.getPlot(); // set the range axis to display integers only... NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false); // the SWTGraphics2D class doesn't handle GradientPaint well, so // replace the gradient painter from the default theme with a // standard painter... renderer.setBarPainter(new StandardBarPainter()); CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 6.0)); // OPTIONAL CUSTOMISATION COMPLETED. return chart; }
From source file:eu.delving.sip.base.ReportChartHelper.java
private static JPanel finishBarChart(JFreeChart chart, Color... colors) { CategoryPlot plot = (CategoryPlot) chart.getPlot(); plot.setRangeAxisLocation(AxisLocation.BOTTOM_OR_LEFT); plot.setRangePannable(true);//w w w .j a v a 2 s.c o m if (colors.length > 0) plot.setRenderer(new CustomRenderer(colors)); BarRenderer bar = (BarRenderer) plot.getRenderer(); bar.setItemLabelAnchorOffset(9D); bar.setBaseItemLabelsVisible(true); bar.setBaseItemLabelGenerator(new StandardCategoryItemLabelGenerator()); bar.setMaximumBarWidth(0.05); bar.setItemMargin(0.03D); bar.setBasePositiveItemLabelPosition( new ItemLabelPosition(INSIDE12, CENTER_RIGHT, CENTER_RIGHT, -1.5707963267948966D)); bar.setPositiveItemLabelPositionFallback( new ItemLabelPosition(OUTSIDE12, CENTER_LEFT, CENTER_LEFT, -1.5707963267948966D)); CategoryAxis x = plot.getDomainAxis(); x.setCategoryLabelPositions(CategoryLabelPositions.DOWN_90); x.setCategoryMargin(0.25D); x.setUpperMargin(0.02D); x.setLowerMargin(0.02D); NumberAxis y = (NumberAxis) plot.getRangeAxis(); y.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); y.setUpperMargin(0.10000000000000001D); ChartUtilities.applyCurrentTheme(chart); return new ChartPanel(chart); }
From source file:org.jfree.experimental.chart.swt.demo.SWTBarChartDemo1.java
/** * Creates a sample chart./*from w w w.j ava2 s. com*/ * * @param dataset the dataset. * * @return The chart. */ private static JFreeChart createChart(CategoryDataset dataset) { // create the chart... JFreeChart chart = ChartFactory.createBarChart("SWTBarChartDemo1", // chart title "Category", // domain axis label "Value", // range axis label dataset, // data PlotOrientation.VERTICAL, // orientation true, // include legend true, // tooltips? false // URLs? ); // NOW DO SOME OPTIONAL CUSTOMISATION OF THE CHART... // get a reference to the plot for further customisation... CategoryPlot plot = (CategoryPlot) chart.getPlot(); // set the range axis to display integers only... NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); // disable bar outlines... BarRenderer renderer = (BarRenderer) plot.getRenderer(); renderer.setDrawBarOutline(false); // the SWTGraphics2D class doesn't handle GradientPaint well, so // replace the gradient painter from the default theme with a // standard painter... renderer.setBarPainter(new StandardBarPainter()); CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(Math.PI / 6.0)); // OPTIONAL CUSTOMISATION COMPLETED. return chart; }
From source file:graficos.GraficoBarras.java
private static JFreeChart crearGrafico(CategoryDataset cjto_datos) { JFreeChart grafico = ChartFactory.createBarChart3D("Distribucin de Recursos", // Ttulo "Unidad de tiempo", // Ttulo eje x "Recurso", // Ttulo eje y cjto_datos, // Datos PlotOrientation.VERTICAL, // Orientacin true, // Incluir leyenda true, // Incluir tooltips false // Incluir URLs );// ww w . j a v a2 s. c om grafico.setBackgroundPaint(new Color(240, 240, 240)); grafico.getPlot().zoom(0.0); CategoryPlot ploter = (CategoryPlot) grafico.getPlot(); NumberAxis3D rangeAxis = (NumberAxis3D) ploter.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis3D.createIntegerTickUnits()); BarRenderer3D renderer = (BarRenderer3D) ploter.getRenderer(); renderer.setDrawBarOutline(false); GradientPaint gp0 = new GradientPaint(0.0f, 0.0f, Color.blue, 0.0f, 0.0f, new Color(0, 0, 64)); GradientPaint gp1 = new GradientPaint(0.0f, 0.0f, Color.green, 0.0f, 0.0f, new Color(0, 64, 0)); renderer.setSeriesPaint(0, gp0); renderer.setSeriesPaint(1, gp1); renderer.setItemMargin(0.0); CategoryAxis domainAxis = ploter.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.createUpRotationLabelPositions(0.0)); return grafico; }
From source file:org.jfree.chart.demo.ParetoChartDemo1.java
public static JFreeChart createChart(CategoryDataset acategorydataset[]) { JFreeChart jfreechart = ChartFactory.createBarChart("Freshmeat Software Projects", "Language", "Projects", acategorydataset[0], PlotOrientation.VERTICAL, true, true, false); jfreechart.addSubtitle(new TextTitle("By Programming Language")); jfreechart.addSubtitle(new TextTitle("As at 5 March 2003")); jfreechart.setBackgroundPaint(Color.white); CategoryPlot categoryplot = (CategoryPlot) jfreechart.getPlot(); categoryplot.setBackgroundPaint(Color.lightGray); categoryplot.setRangeGridlinePaint(Color.white); CategoryAxis categoryaxis = categoryplot.getDomainAxis(); categoryaxis.setLowerMargin(0.02D);/*w w w . ja v a 2s . com*/ categoryaxis.setUpperMargin(0.02D); categoryaxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90); NumberAxis numberaxis = (NumberAxis) categoryplot.getRangeAxis(); numberaxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); LineAndShapeRenderer lineandshaperenderer = new LineAndShapeRenderer(); NumberAxis numberaxis1 = new NumberAxis("Percent"); numberaxis1.setNumberFormatOverride(NumberFormat.getPercentInstance()); categoryplot.setRangeAxis(1, numberaxis1); categoryplot.setDataset(1, acategorydataset[1]); categoryplot.setRenderer(1, lineandshaperenderer); categoryplot.mapDatasetToRangeAxis(1, 1); categoryplot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD); return jfreechart; }