List of usage examples for org.jfree.chart.renderer.category ScatterRenderer setSeriesShape
public void setSeriesShape(int series, Shape shape)
From source file:com.rapidminer.gui.new_plotter.engine.jfreechart.ChartRendererFactory.java
private static void configureScatterRenderer(ScatterRenderer renderer, ValueSource valueSource, PlotInstance plotInstance) throws ChartPlottimeException { ValueSourceData valueSourceData = plotInstance.getPlotData().getValueSourceData(valueSource); int seriesCount = valueSourceData.getSeriesCount(); SeriesFormat seriesFormat = valueSource.getSeriesFormat(); DimensionConfig domainConfig = valueSource.getDomainConfig(); DimensionConfig colorDimensionConfig = plotInstance.getCurrentPlotConfigurationClone() .getDimensionConfig(PlotDimension.COLOR); DimensionConfig shapeDimensionConfig = plotInstance.getCurrentPlotConfigurationClone() .getDimensionConfig(PlotDimension.SHAPE); renderer.setDefaultEntityRadius(4);//w w w.j a v a 2 s .co m // loop all series and set series format for (int seriesIdx = 0; seriesIdx < seriesCount; ++seriesIdx) { // lines are not supported in a ScatterRenderer, but this is already checked in // JFreeChartPlotEngine.getWarnings(). // configure series shape if necessary if (!SeriesFormat.calculateIndividualFormatForEachItem(domainConfig, shapeDimensionConfig)) { // if(seriesFormat.getItemShape() != ItemShape.NONE) { renderer.setSeriesShape(seriesIdx, seriesFormat.getItemShape().getShape()); // } else { // throw new ChartPlottimeException("unsupported_item_shape", // valueSource.toString(), seriesFormat.getItemShape()); // } } // configure series color if necessary if (!SeriesFormat.calculateIndividualFormatForEachItem(domainConfig, colorDimensionConfig)) { Color itemColor = seriesFormat.getItemColor(); renderer.setSeriesPaint(seriesIdx, itemColor); } renderer.setSeriesOutlinePaint(seriesIdx, PlotConfiguration.DEFAULT_SERIES_OUTLINE_PAINT); renderer.setUseOutlinePaint(true); renderer.setDrawOutlines(true); renderer.setUseSeriesOffset(false); } }
From source file:ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController.java
private boolean writeDetailedFactorAnalysis(ExpressionExperiment ee, OutputStream os) throws Exception { SVDValueObject svdo = svdService.getSvdFactorAnalysis(ee.getId()); if (svdo == null) return false; if (svdo.getFactors().isEmpty() && svdo.getDates().isEmpty()) { return false; }//from w ww . j a v a 2 s . c om Map<Integer, Map<Long, Double>> factorCorrelations = svdo.getFactorCorrelations(); // Map<Integer, Map<Long, Double>> factorPvalues = svdo.getFactorPvalues(); Map<Integer, Double> dateCorrelations = svdo.getDateCorrelations(); assert ee.getId().equals(svdo.getId()); ee = expressionExperimentService.thawLite(ee); // need the experimental design int maxWidth = 30; Map<Long, String> efs = this.getFactorNames(ee, maxWidth); Map<Long, ExperimentalFactor> efIdMap = EntityUtils .getIdMap(ee.getExperimentalDesign().getExperimentalFactors()); Collection<Long> continuousFactors = new HashSet<>(); for (ExperimentalFactor ef : ee.getExperimentalDesign().getExperimentalFactors()) { boolean isContinous = ExperimentalDesignUtils.isContinuous(ef); if (isContinous) { continuousFactors.add(ef.getId()); } } /* * Make plots of the dates vs. PCs, factors vs. PCs. */ int MAX_COMP = 3; Map<Long, List<JFreeChart>> charts = new LinkedHashMap<>(); ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme()); /* * FACTORS */ String componentShorthand = "PC"; for (Integer component : factorCorrelations.keySet()) { if (component >= MAX_COMP) break; String xaxisLabel = componentShorthand + (component + 1); for (Long efId : factorCorrelations.get(component).keySet()) { /* * Should not happen. */ if (!efs.containsKey(efId)) { log.warn("No experimental factor with id " + efId); continue; } if (!svdo.getFactors().containsKey(efId)) { // this should not happen. continue; } boolean isCategorical = !continuousFactors.contains(efId); Map<Long, String> categories = new HashMap<>(); if (isCategorical) { this.getCategories(efIdMap, efId, categories); } if (!charts.containsKey(efId)) { charts.put(efId, new ArrayList<JFreeChart>()); } Double a = factorCorrelations.get(component).get(efId); String plotname = (efs.get(efId) == null ? "?" : efs.get(efId)) + " " + xaxisLabel; // unique? if (a != null && !Double.isNaN(a)) { String title = plotname + " " + String.format("%.2f", a); List<Double> values = svdo.getFactors().get(efId); Double[] eigenGene = this.getEigenGene(svdo, component); assert values.size() == eigenGene.length; /* * Plot eigengene vs values, add correlation to the plot */ JFreeChart chart; if (isCategorical) { /* * Categorical factor */ // use the absolute value of the correlation, since direction is arbitrary. title = plotname + " " + String.format("r=%.2f", Math.abs(a)); DefaultMultiValueCategoryDataset dataset = new DefaultMultiValueCategoryDataset(); /* * What this code does is organize the factor values by the groups. */ Map<String, List<Double>> groupedValues = new TreeMap<>(); for (int i = 0; i < values.size(); i++) { Long fvId = values.get(i).longValue(); String fvValue = categories.get(fvId); if (fvValue == null) { /* * Problem ...eg gill2006fateinocean id=1748 -- missing values. We just don't plot * anything for this sample. */ continue; // is this all we need to do? } if (!groupedValues.containsKey(fvValue)) { groupedValues.put(fvValue, new ArrayList<Double>()); } groupedValues.get(fvValue).add(eigenGene[i]); if (log.isDebugEnabled()) log.debug(fvValue + " " + values.get(i)); } for (String key : groupedValues.keySet()) { dataset.add(groupedValues.get(key), plotname, key); } // don't show the name of the X axis: it's redundant with the title. NumberAxis rangeAxis = new NumberAxis(xaxisLabel); rangeAxis.setAutoRangeIncludesZero(false); // rangeAxis.setAutoRange( false ); rangeAxis.setAutoRangeMinimumSize(4.0); // rangeAxis.setRange( new Range( -2, 2 ) ); CategoryPlot plot = new CategoryPlot(dataset, new CategoryAxis(null), rangeAxis, new ScatterRenderer()); plot.setRangeGridlinesVisible(false); plot.setDomainGridlinesVisible(false); chart = new JFreeChart(title, new Font("SansSerif", Font.BOLD, 12), plot, false); ScatterRenderer renderer = (ScatterRenderer) plot.getRenderer(); float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP); renderer.setSeriesFillPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f)); renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3)); renderer.setUseOutlinePaint(false); renderer.setUseFillPaint(true); renderer.setBaseFillPaint(Color.white); CategoryAxis domainAxis = plot.getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45); } else { /* * Continuous value factor */ DefaultXYDataset series = new DefaultXYDataset(); series.addSeries(plotname, new double[][] { ArrayUtils.toPrimitive(values.toArray(new Double[] {})), ArrayUtils.toPrimitive(eigenGene) }); // don't show x-axis label, which would otherwise be efs.get( efId ) chart = ChartFactory.createScatterPlot(title, null, xaxisLabel, series, PlotOrientation.VERTICAL, false, false, false); XYPlot plot = chart.getXYPlot(); plot.setRangeGridlinesVisible(false); plot.setDomainGridlinesVisible(false); XYItemRenderer renderer = plot.getRenderer(); renderer.setBasePaint(Color.white); renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3)); float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP); renderer.setSeriesPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f)); plot.setRenderer(renderer); } chart.getTitle().setFont(new Font("SansSerif", Font.BOLD, 12)); charts.get(efId).add(chart); } } } /* * DATES */ charts.put(-1L, new ArrayList<JFreeChart>()); for (Integer component : dateCorrelations.keySet()) { String xaxisLabel = componentShorthand + (component + 1); List<Date> dates = svdo.getDates(); if (dates.isEmpty()) break; long secspan = ubic.basecode.util.DateUtil.numberOfSecondsBetweenDates(dates); if (component >= MAX_COMP) break; Double a = dateCorrelations.get(component); if (a != null && !Double.isNaN(a)) { Double[] eigenGene = svdo.getvMatrix().getColObj(component); /* * Plot eigengene vs values, add correlation to the plot */ TimeSeries series = new TimeSeries("Dates vs. eigen" + (component + 1)); int i = 0; for (Date d : dates) { // if span is less than an hour, retain the minute. if (secspan < 60 * 60) { series.addOrUpdate(new Minute(d), eigenGene[i++]); } else { series.addOrUpdate(new Hour(d), eigenGene[i++]); } } TimeSeriesCollection dataset = new TimeSeriesCollection(); dataset.addSeries(series); JFreeChart chart = ChartFactory.createTimeSeriesChart( "Dates: " + xaxisLabel + " " + String.format("r=%.2f", a), null, xaxisLabel, dataset, false, false, false); XYPlot xyPlot = chart.getXYPlot(); chart.getTitle().setFont(new Font("SansSerif", Font.BOLD, 12)); // standard renderer makes lines. XYDotRenderer renderer = new XYDotRenderer(); renderer.setBaseFillPaint(Color.white); renderer.setDotHeight(3); renderer.setDotWidth(3); renderer.setSeriesShape(0, new Ellipse2D.Double(0, 0, 3, 3)); // has no effect, need dotheight. float saturationDrop = (float) Math.min(1.0, component * 0.8f / MAX_COMP); renderer.setSeriesPaint(0, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f)); ValueAxis domainAxis = xyPlot.getDomainAxis(); domainAxis.setVerticalTickLabels(true); xyPlot.setRenderer(renderer); xyPlot.setRangeGridlinesVisible(false); xyPlot.setDomainGridlinesVisible(false); charts.get(-1L).add(chart); } } /* * Plot in a grid, with each factor as a column. FIXME What if we have too many factors to fit on the screen? */ int columns = (int) Math.ceil(charts.size()); int perChartSize = ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX; BufferedImage image = new BufferedImage(columns * perChartSize, MAX_COMP * perChartSize, BufferedImage.TYPE_INT_ARGB); Graphics2D g2 = image.createGraphics(); int currentX = 0; int currentY = 0; for (Long id : charts.keySet()) { for (JFreeChart chart : charts.get(id)) { this.addChartToGraphics(chart, g2, currentX, currentY, perChartSize, perChartSize); if (currentY + perChartSize < MAX_COMP * perChartSize) { currentY += perChartSize; } else { currentY = 0; currentX += perChartSize; } } } os.write(ChartUtilities.encodeAsPNG(image)); return true; }