List of usage examples for org.jfree.chart.plot XYPlot setNoDataMessage
public void setNoDataMessage(String message)
null, and sends a PlotChangeEvent to all registered listeners. From source file:org.esa.beam.visat.toolviews.stat.HistogramPanel.java
private ChartPanel createChartPanel(JFreeChart chart) { XYPlot plot = chart.getXYPlot(); plot.setForegroundAlpha(0.85f);/*w w w. j a v a 2s . c om*/ plot.setNoDataMessage(NO_DATA_MESSAGE); plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5)); ChartPanel chartPanel = new ChartPanel(chart); MaskSelectionToolSupport maskSelectionToolSupport = new MaskSelectionToolSupport(this, chartPanel, "histogram_plot_area", "Mask generated from selected histogram plot area", Color.RED, PlotAreaSelectionTool.AreaType.X_RANGE) { @Override protected String createMaskExpression(PlotAreaSelectionTool.AreaType areaType, Shape shape) { Rectangle2D bounds = shape.getBounds2D(); return createMaskExpression(bounds.getMinX(), bounds.getMaxX()); } protected String createMaskExpression(double x1, double x2) { String bandName = BandArithmetic.createExternalName(getRaster().getName()); HistogramPanelModel.HistogramConfig currentConfig = createHistogramConfig(); return String.format("%s >= %s && %s <= %s", bandName, model.hasStx(currentConfig) ? model.getStx(currentConfig).getHistogramScaling().scaleInverse(x1) : x1, bandName, model.hasStx(currentConfig) ? model.getStx(currentConfig).getHistogramScaling().scaleInverse(x2) : x2); } }; chartPanel.getPopupMenu().addSeparator(); chartPanel.getPopupMenu().add(maskSelectionToolSupport.createMaskSelectionModeMenuItem()); chartPanel.getPopupMenu().add(maskSelectionToolSupport.createDeleteMaskMenuItem()); chartPanel.getPopupMenu().addSeparator(); chartPanel.getPopupMenu().add(createCopyDataToClipboardMenuItem()); return chartPanel; }
From source file:org.openmrs.web.servlet.ShowGraphServlet.java
/** * The main method for this class. It will create a JFreeChart object to be written to the * response.//from w ww . jav a 2 s . c om * * @param request the current request will all the parameters needed * @return JFreeChart object to be rendered * @should set value axis label to given units * @should set value axis label to concept numeric units if given units is null */ protected JFreeChart getChart(HttpServletRequest request) { // All available GET parameters String patientId = request.getParameter("patientId"); // required String conceptId1 = request.getParameter("conceptId"); // required String conceptId2 = request.getParameter("conceptId2"); String chartTitle = request.getParameter("chartTitle"); String units = request.getParameter("units"); String minRangeString = request.getParameter("minRange"); String maxRangeString = request.getParameter("maxRange"); String hideDate = request.getParameter("hideDate"); Patient patient = Context.getPatientService().getPatient(Integer.parseInt(patientId)); // Set date range to passed values, otherwise set a default date range to the last 12 months Calendar cal = Calendar.getInstance(); Date fromDate = getFromDate(request.getParameter("fromDate")); Date toDate = getToDate(request.getParameter("toDate")); // Swap if fromDate is after toDate if (fromDate.getTime() > toDate.getTime()) { Long temp = fromDate.getTime(); fromDate.setTime(toDate.getTime()); toDate.setTime(temp); } // Graph parameters Double minRange = null; Double maxRange = null; Double normalLow = null; Double normalHigh = null; Double criticalLow = null; Double criticalHigh = null; String timeAxisTitle = null; String rangeAxisTitle = null; boolean userSpecifiedMaxRange = false; boolean userSpecifiedMinRange = false; // Fetching obs List<Obs> observations1 = new ArrayList<Obs>(); List<Obs> observations2 = new ArrayList<Obs>(); Concept concept1 = null, concept2 = null; if (conceptId1 != null) { concept1 = Context.getConceptService().getConcept(Integer.parseInt(conceptId1)); } if (conceptId2 != null) { concept2 = Context.getConceptService().getConcept(Integer.parseInt(conceptId2)); } if (concept1 != null) { observations1 = Context.getObsService().getObservationsByPersonAndConcept(patient, concept1); chartTitle = concept1.getName().getName(); rangeAxisTitle = ((ConceptNumeric) concept1).getUnits(); minRange = ((ConceptNumeric) concept1).getLowAbsolute(); maxRange = ((ConceptNumeric) concept1).getHiAbsolute(); normalLow = ((ConceptNumeric) concept1).getLowNormal(); normalHigh = ((ConceptNumeric) concept1).getHiNormal(); criticalLow = ((ConceptNumeric) concept1).getLowCritical(); criticalHigh = ((ConceptNumeric) concept1).getHiCritical(); // Only get observations2 if both concepts share the same units; update chart title and ranges if (concept2 != null) { String concept2Units = ((ConceptNumeric) concept2).getUnits(); if (concept2Units != null && concept2Units.equals(rangeAxisTitle)) { observations2 = Context.getObsService().getObservationsByPersonAndConcept(patient, concept2); chartTitle += " + " + concept2.getName().getName(); if (((ConceptNumeric) concept2).getHiAbsolute() != null && ((ConceptNumeric) concept2).getHiAbsolute() > maxRange) { maxRange = ((ConceptNumeric) concept2).getHiAbsolute(); } if (((ConceptNumeric) concept2).getLowAbsolute() != null && ((ConceptNumeric) concept2).getLowAbsolute() < minRange) { minRange = ((ConceptNumeric) concept2).getLowAbsolute(); } } else { log.warn("Units for concept id: " + conceptId2 + " don't match units for concept id: " + conceptId1 + ". Only displaying " + conceptId1); concept2 = null; // nullify concept2 so that the legend isn't shown later } } } else { chartTitle = "Concept " + conceptId1 + " not found"; rangeAxisTitle = "Value"; } // Overwrite with user-specified values, otherwise use default values if (units != null && units.length() > 0) { rangeAxisTitle = units; } if (minRangeString != null) { minRange = Double.parseDouble(minRangeString); userSpecifiedMinRange = true; } if (maxRangeString != null) { maxRange = Double.parseDouble(maxRangeString); userSpecifiedMaxRange = true; } if (chartTitle == null) { chartTitle = ""; } if (rangeAxisTitle == null) { rangeAxisTitle = ""; } if (minRange == null) { minRange = 0.0; } if (maxRange == null) { maxRange = 200.0; } // Create data set TimeSeriesCollection dataset = new TimeSeriesCollection(); TimeSeries series1, series2; // Interval-dependent units Class<? extends RegularTimePeriod> timeScale = null; if (toDate.getTime() - fromDate.getTime() <= 86400000) { // Interval <= 1 day: minutely timeScale = Minute.class; timeAxisTitle = "Time"; } else if (toDate.getTime() - fromDate.getTime() <= 259200000) { // Interval <= 3 days: hourly timeScale = Hour.class; timeAxisTitle = "Time"; } else { timeScale = Day.class; timeAxisTitle = "Date"; } if (concept1 == null) { series1 = new TimeSeries("NULL", Hour.class); } else { series1 = new TimeSeries(concept1.getName().getName(), timeScale); } if (concept2 == null) { series2 = new TimeSeries("NULL", Hour.class); } else { series2 = new TimeSeries(concept2.getName().getName(), timeScale); } // Add data points for concept1 for (Obs obs : observations1) { if (obs.getValueNumeric() != null && obs.getObsDatetime().getTime() >= fromDate.getTime() && obs.getObsDatetime().getTime() < toDate.getTime()) { cal.setTime(obs.getObsDatetime()); if (timeScale == Minute.class) { Minute min = new Minute(cal.get(Calendar.MINUTE), cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series1.addOrUpdate(min, obs.getValueNumeric()); } else if (timeScale == Hour.class) { Hour hour = new Hour(cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series1.addOrUpdate(hour, obs.getValueNumeric()); } else { Day day = new Day(cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series1.addOrUpdate(day, obs.getValueNumeric()); } } } // Add data points for concept2 for (Obs obs : observations2) { if (obs.getValueNumeric() != null && obs.getObsDatetime().getTime() >= fromDate.getTime() && obs.getObsDatetime().getTime() < toDate.getTime()) { cal.setTime(obs.getObsDatetime()); if (timeScale == Minute.class) { Minute min = new Minute(cal.get(Calendar.MINUTE), cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series2.addOrUpdate(min, obs.getValueNumeric()); } else if (timeScale == Hour.class) { Hour hour = new Hour(cal.get(Calendar.HOUR_OF_DAY), cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series2.addOrUpdate(hour, obs.getValueNumeric()); } else { Day day = new Day(cal.get(Calendar.DAY_OF_MONTH), cal.get(Calendar.MONTH) + 1, cal.get(Calendar.YEAR)); series2.addOrUpdate(day, obs.getValueNumeric()); } } } // Add series to dataset dataset.addSeries(series1); if (!series2.isEmpty()) { dataset.addSeries(series2); } // As of JFreeChart 1.0.11 the default background color is dark grey instead of white. // This line restores the original white background. ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme()); JFreeChart chart = null; // Show legend only if more than one series if (concept2 == null) { chart = ChartFactory.createTimeSeriesChart(chartTitle, timeAxisTitle, rangeAxisTitle, dataset, false, false, false); } else { chart = ChartFactory.createTimeSeriesChart(chartTitle, timeAxisTitle, rangeAxisTitle, dataset, true, false, false); } // Customize title font Font font = new Font("Arial", Font.BOLD, 12); TextTitle title = chart.getTitle(); title.setFont(font); chart.setTitle(title); // Add subtitle, unless 'hideDate' has been passed if (hideDate == null) { TextTitle subtitle = new TextTitle(fromDate.toString() + " - " + toDate.toString()); subtitle.setFont(font); chart.addSubtitle(subtitle); } XYPlot plot = (XYPlot) chart.getPlot(); plot.setNoDataMessage("No Data Available"); // Add abnormal/critical range background color (only for single-concept graphs) if (concept2 == null) { IntervalMarker abnormalLow, abnormalHigh, critical; if (normalHigh != null) { abnormalHigh = new IntervalMarker(normalHigh, maxRange, COLOR_ABNORMAL); plot.addRangeMarker(abnormalHigh); } if (normalLow != null) { abnormalLow = new IntervalMarker(minRange, normalLow, COLOR_ABNORMAL); plot.addRangeMarker(abnormalLow); } if (criticalHigh != null) { critical = new IntervalMarker(criticalHigh, maxRange, COLOR_CRITICAL); plot.addRangeMarker(critical); } if (criticalLow != null) { critical = new IntervalMarker(minRange, criticalLow, COLOR_CRITICAL); plot.addRangeMarker(critical); } // there is data outside of the absolute lower limits for this concept (or of what the user specified as minrange) if (plot.getRangeAxis().getLowerBound() < minRange) { IntervalMarker error = new IntervalMarker(plot.getRangeAxis().getLowerBound(), minRange, COLOR_ERROR); plot.addRangeMarker(error); } if (plot.getRangeAxis().getUpperBound() > maxRange) { IntervalMarker error = new IntervalMarker(maxRange, plot.getRangeAxis().getUpperBound(), COLOR_ERROR); plot.addRangeMarker(error); } } // Visuals XYItemRenderer r = plot.getRenderer(); if (r instanceof XYLineAndShapeRenderer) { XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) r; renderer.setBaseShapesFilled(true); renderer.setBaseShapesVisible(true); } // Customize the plot (range and domain axes) // Modify x-axis (datetime) DateAxis timeAxis = (DateAxis) plot.getDomainAxis(); if (timeScale == Day.class) { timeAxis.setDateFormatOverride(new SimpleDateFormat("dd-MMM-yyyy")); } timeAxis.setRange(fromDate, toDate); // Set y-axis range (values) NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); rangeAxis.setStandardTickUnits(NumberAxis.createIntegerTickUnits()); if (userSpecifiedMinRange) { minRange = (rangeAxis.getLowerBound() < minRange) ? rangeAxis.getLowerBound() : minRange; } if (userSpecifiedMaxRange) { // otherwise we just use default range maxRange = (rangeAxis.getUpperBound() > maxRange) ? rangeAxis.getUpperBound() : maxRange; } rangeAxis.setRange(minRange, maxRange); 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 a va 2s . co 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; }
From source file:gov.nih.nci.ispy.ui.graphing.chart.plot.ISPYCorrelationScatterPlot.java
private void createChart() { String title = "Correlation Scatter Plot correlationCoefficient=" + nf.format(corrValue) + " N=" + dataPoints.size();// w w w . j a va2 s. c o m corrChart = ChartFactory.createScatterPlot(title, xLabel, yLabel, null, PlotOrientation.VERTICAL, true, true, false); XYPlot plot = (XYPlot) corrChart.getPlot(); plot.setNoDataMessage(null); XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); renderer.setToolTipGenerator(new StandardXYToolTipGenerator()); renderer.setUseOutlinePaint(true); plot.setRangeCrosshairVisible(false); plot.setDomainCrosshairVisible(false); // XYShapeAnnotation annotation = new XYShapeAnnotation(new Rectangle2D.Double(25.0, 25.0, 5, 5)); // // plot.addAnnotation(annotation); NumberAxis domainAxis = (NumberAxis) plot.getDomainAxis(); NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis(); //should determine axis range using datapoints. List<PlotPoint> plotPoints = new ArrayList<PlotPoint>(dataPoints); DataRange Xrange = PlotPoint.getDataRange(plotPoints, AxisType.X_AXIS); DataRange Yrange = PlotPoint.getDataRange(plotPoints, AxisType.Y_AXIS); // Double xAbsMax = Math.max(Math.abs(Xrange.getMaxRange()), Math.abs(Xrange.getMinRange())); // Double yAbsMax = Math.max(Math.abs(Yrange.getMaxRange()), Math.abs(Yrange.getMinRange())); // // Double maxAbsVal = Math.max(xAbsMax, yAbsMax); domainAxis.setAutoRangeIncludesZero(false); double xTick = 10.0; double yTick = 10.0; double xdist = Math.abs(Xrange.getMaxRange() - Xrange.getMinRange()); double ydist = Math.abs(Yrange.getMaxRange() - Yrange.getMinRange()); if (xdist < 10.0) { xTick = 1.0; } if (ydist < 10.0) { yTick = 1.0; } // if (maxAbsVal <= 25.0) { // tickUnit =5.0; // } // else if (maxAbsVal <= 50.0) { // tickUnit = 10.0; // } domainAxis.setTickUnit(new NumberTickUnit(xTick)); rangeAxis.setTickUnit(new NumberTickUnit(yTick)); //double glyphScaleFactor = (maxAbsVal*2.0)/600.0; //assuming 600 pixels for the graph double xScale = xdist / 600.0; //double glyphScaleFactor = 1.0; double yScale = ydist / 600.0; //double adjAbsVal = Math.ceil(maxAbsVal + (glyphScaleFactor*8.0)); //domainAxis.setRange(-maxAbsVal, maxAbsVal); double xMin = Xrange.getMinRange() - xScale * glyphSize; double xMax = Xrange.getMaxRange() + xScale * glyphSize; double yMin = Yrange.getMinRange() - yScale * glyphSize; double yMax = Yrange.getMaxRange() + yScale * glyphSize; domainAxis.setRange(xMin, xMax); //rangeAxis.setRange(-maxAbsVal, maxAbsVal); rangeAxis.setRange(yMin, yMax); Set<SampleInfo> infoSet = new HashSet<SampleInfo>(); if ((colorBy == ColorByType.IHC_EXPRESSION_X) || (colorBy == ColorByType.IHC_EXPRESSION_Y)) { String geneName = null; if ((colorBy == ColorByType.IHC_EXPRESSION_X) && (ct1 != ContinuousType.GENE)) { logger.info("User attempted to color by ihc x on non gene continuous type."); //need to show validation error return; } else if ((colorBy == ColorByType.IHC_EXPRESSION_Y) && (ct2 != ContinuousType.GENE)) { logger.info("User attempted to color by ihc y on non gene continuous type."); //need to show validation error return; } else { if (colorBy == ColorByType.IHC_EXPRESSION_X) { //parse the gene name from the xLabel geneName = xLabel.substring(0, xLabel.indexOf('_')); } else if (colorBy == ColorByType.IHC_EXPRESSION_Y) { //parse the gene name from the yLabel geneName = yLabel.substring(0, yLabel.indexOf('_')); } } //Get the IHC data for the samples to be graphed LevelOfExpressionIHCService loeService = LevelOfExpressionIHCService.getInstance(); LossOfExpressionIHCService lossService = LossOfExpressionIHCService.getInstance(); Set<String> sampleIds = new HashSet<String>(); String labtrackId; SampleInfo info; for (ISPYPlotPoint corrPoint : dataPoints) { info = corrPoint.getSampleInfo(); if (info != null) { labtrackId = corrPoint.getSampleInfo().getLabtrackId(); sampleIds.add(labtrackId); infoSet.add(info); } else { logger.warn("Point id=" + corrPoint.getId() + " has no sample info. Skipping point"); } } Collection<? extends Finding> loeFindings = loeService.getFindingsFromSampleInfo(infoSet); Collection<? extends Finding> lossFindings = lossService.getFindingsFromSampleInfo(infoSet); List<IHCFinding> findings = new ArrayList<IHCFinding>(); for (Finding f : loeFindings) { findings.add((IHCFinding) f); } for (Finding f : lossFindings) { findings.add((IHCFinding) f); } // Need to handle mapping names to IHC biomarker names. //EGFR (ok), FAK (PTK2), HER2 (ERBB2), Ki-67, P53, bcl2 (ok), p27, CYCLIN_D1 (CCND1) //Translate the gene names into the biomarker names //used by ihc. This code should be removed once protein biomarker //alias is implmented. String ihcBiomarker = geneName; if (geneName.equalsIgnoreCase("PTK2")) { ihcBiomarker = "FAK"; ihcBiomarkerType = IHCBiomarkerType.FAK; } else if (geneName.equalsIgnoreCase("ERBB2")) { ihcBiomarker = "HER2"; ihcBiomarkerType = IHCBiomarkerType.HER2; } else if (geneName.equalsIgnoreCase("MKI67")) { //need to check this one ihcBiomarker = "Ki-67"; ihcBiomarkerType = IHCBiomarkerType.KI67; } else if (geneName.equalsIgnoreCase("TP53")) { ihcBiomarker = "P53"; ihcBiomarkerType = IHCBiomarkerType.P53; } else if (geneName.equalsIgnoreCase("Cdkn1b")) { ihcBiomarker = "P27"; ihcBiomarkerType = IHCBiomarkerType.P27; } else if (geneName.equalsIgnoreCase("BCL2")) { ihcBiomarker = "BCL2"; ihcBiomarkerType = IHCBiomarkerType.BCL2; } else if (geneName.equalsIgnoreCase("EGFR")) { ihcBiomarker = "EGFR"; ihcBiomarkerType = IHCBiomarkerType.EGFR; } else if (geneName.equalsIgnoreCase("CCND1")) { ihcBiomarker = "CYCLIN_D1"; ihcBiomarkerType = IHCBiomarkerType.CYCLIN_D1; } List<IHCFinding> filteredList = getIHCFindingsForBiomarker(findings, ihcBiomarker); //TEST Case // Set<String> testIds = new HashSet<String>(); // testIds.add("212833"); // testIds.add("213152"); //Collection<? extends Finding> loeFindings = loeService.getFindingsFromSampleIds(testIds); //Collection<? extends Finding> lossFindings = lossService.getFindingsFromSampleIds(sampleIds); ihcData = new HashMap<String, List<IHCFinding>>(); IHCFinding loeFinding; List<IHCFinding> findingList; Specimen specimen = null; String patientDID = null; for (Finding finding : filteredList) { loeFinding = (IHCFinding) finding; specimen = loeFinding.getSpecimen(); if ((specimen != null) && (specimen.getPatientDID() != null)) { patientDID = specimen.getPatientDID(); findingList = ihcData.get(patientDID); if (findingList == null) { findingList = new ArrayList<IHCFinding>(); ihcData.put(patientDID, findingList); } findingList.add(loeFinding); } else { logger.warn( "loeFinding id=" + loeFinding.getId() + " has null specimen or patientDID. Skipping.."); } } // IHCFinding lossFinding; // for (Finding finding : lossFindings) { // lossFinding = (IHCFinding) finding; // ihcData.put(lossFinding.getId(), lossFinding); // } } createGlyphsAndAddToPlot(plot, xScale, yScale); // Paint p = new GradientPaint(0, 0, Color.white, 1000, 0, Color.green); //try and match the UI e9e9e9 Paint p = new Color(233, 233, 233); corrChart.setBackgroundPaint(p); buildLegend(); }
From source file:ec.util.chart.swing.JTimeSeriesChart.java
private void onNoDataMessageChange(XYPlot plot) { plot.setNoDataMessage(noDataMessage); }
From source file:org.eumetsat.metop.visat.SounderInfoView.java
protected void configureSpectrumPlot(XYPlot plot) { plot.setBackgroundPaint(Color.lightGray); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); plot.setDomainGridlinePaint(Color.white); plot.setRangeGridlinePaint(Color.white); plot.setDomainCrosshairVisible(true); plot.setDomainCrosshairLockedOnData(true); plot.setRangeCrosshairVisible(false); plot.setNoDataMessage(NO_IFOV_SELECTED); }
From source file:org.eumetsat.metop.visat.IasiInfoView.java
private void configureSpectrumPlot(XYPlot plot) { plot.setBackgroundPaint(Color.lightGray); plot.setAxisOffset(new RectangleInsets(5.0, 5.0, 5.0, 5.0)); plot.setDomainGridlinePaint(Color.white); plot.setRangeGridlinePaint(Color.white); plot.setDomainCrosshairVisible(true); plot.setDomainCrosshairLockedOnData(true); plot.setRangeCrosshairVisible(false); plot.setNoDataMessage(NO_IFOV_SELECTED); }
From source file:net.sourceforge.processdash.ev.ui.ScheduleBalancingDialog.java
private void addChartToPanel(JPanel panel, int gridY) { // create a dataset for displaying schedule data chartData = new ChartData(); updateChart();// w w w. j av a2 s . c o m // customize a renderer for displaying schedules XYBarRenderer renderer = new XYBarRenderer(); renderer.setUseYInterval(true); renderer.setBaseToolTipGenerator(chartData); renderer.setDrawBarOutline(true); // use an inverted, unadorned numeric Y-axis NumberAxis yAxis = new NumberAxis(); yAxis.setInverted(true); yAxis.setTickLabelsVisible(false); yAxis.setTickMarksVisible(false); yAxis.setUpperMargin(0); // use a Date-based X-axis DateAxis xAxis = new DateAxis(); // create an XY plot to display the data XYPlot plot = new XYPlot(chartData, xAxis, yAxis, renderer); plot.setOrientation(PlotOrientation.VERTICAL); plot.setRangeGridlinesVisible(false); plot.setNoDataMessage(TaskScheduleDialog.resources.getString("Chart.No_Data_Message")); // create a chart and a chart panel JFreeChart chart = new JFreeChart(plot); chart.removeLegend(); ChartPanel chartPanel = new ChartPanel(chart); chartPanel.setInitialDelay(50); chartPanel.setDismissDelay(60000); chartPanel.setMinimumDrawHeight(40); chartPanel.setMinimumDrawWidth(40); chartPanel.setMaximumDrawHeight(3000); chartPanel.setMaximumDrawWidth(3000); chartPanel.setPreferredSize(new Dimension(300, gridY * 25)); // add the chart to the dialog content pane GridBagConstraints c = new GridBagConstraints(); c.gridy = gridY; c.gridwidth = 4; c.weightx = 2; c.weighty = 1; c.fill = GridBagConstraints.BOTH; c.insets = new Insets(10, 0, 0, 0); panel.add(chartPanel, c); // retrieve the colors used for each chart bar, and register those // colors with the schedule rows so they can act as a legend for (int i = scheduleRows.size(); i-- > 0;) { ScheduleTableRow oneRow = scheduleRows.get(i); oneRow.addColoredIcon(renderer.lookupSeriesPaint(i)); } }
From source file:org.esa.snap.rcp.statistics.ScatterPlotPanel.java
private void createUI() { final XYPlot plot = getPlot(); plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5)); plot.setNoDataMessage(NO_DATA_MESSAGE); int confidenceDSIndex = 0; int regressionDSIndex = 1; int scatterpointsDSIndex = 2; plot.setDataset(confidenceDSIndex, acceptableDeviationDataset); plot.setDataset(regressionDSIndex, regressionDataset); plot.setDataset(scatterpointsDSIndex, scatterpointsDataset); plot.addAnnotation(r2Annotation); final DeviationRenderer identityRenderer = new DeviationRenderer(true, false); identityRenderer.setSeriesPaint(0, StatisticChartStyling.SAMPLE_DATA_PAINT); identityRenderer.setSeriesFillPaint(0, StatisticChartStyling.SAMPLE_DATA_FILL_PAINT); plot.setRenderer(confidenceDSIndex, identityRenderer); final DeviationRenderer regressionRenderer = new DeviationRenderer(true, false); regressionRenderer.setSeriesPaint(0, StatisticChartStyling.REGRESSION_DATA_PAINT); regressionRenderer.setSeriesFillPaint(0, StatisticChartStyling.REGRESSION_DATA_FILL_PAINT); plot.setRenderer(regressionDSIndex, regressionRenderer); final XYErrorRenderer scatterPointsRenderer = new XYErrorRenderer(); scatterPointsRenderer.setDrawXError(true); scatterPointsRenderer.setErrorStroke(new BasicStroke(1)); scatterPointsRenderer.setErrorPaint(StatisticChartStyling.CORRELATIVE_POINT_OUTLINE_PAINT); scatterPointsRenderer.setSeriesShape(0, StatisticChartStyling.CORRELATIVE_POINT_SHAPE); scatterPointsRenderer.setSeriesOutlinePaint(0, StatisticChartStyling.CORRELATIVE_POINT_OUTLINE_PAINT); scatterPointsRenderer.setSeriesFillPaint(0, StatisticChartStyling.CORRELATIVE_POINT_FILL_PAINT); scatterPointsRenderer.setSeriesLinesVisible(0, false); scatterPointsRenderer.setSeriesShapesVisible(0, true); scatterPointsRenderer.setSeriesOutlineStroke(0, new BasicStroke(1.0f)); scatterPointsRenderer.setSeriesToolTipGenerator(0, (dataset, series, item) -> { final XYIntervalSeriesCollection collection = (XYIntervalSeriesCollection) dataset; final Comparable key = collection.getSeriesKey(series); final double xValue = collection.getXValue(series, item); final double endYValue = collection.getEndYValue(series, item); final double yValue = collection.getYValue(series, item); return String.format("%s: mean = %6.2f, sigma = %6.2f | %s: value = %6.2f", getRasterName(), yValue, endYValue - yValue, key, xValue); });//from w w w . jav a2s .c o m plot.setRenderer(scatterpointsDSIndex, scatterPointsRenderer); final boolean autoRangeIncludesZero = false; final boolean xLog = scatterPlotModel.xAxisLogScaled; final boolean yLog = scatterPlotModel.yAxisLogScaled; plot.setDomainAxis( StatisticChartStyling.updateScalingOfAxis(xLog, plot.getDomainAxis(), autoRangeIncludesZero)); plot.setRangeAxis( StatisticChartStyling.updateScalingOfAxis(yLog, plot.getRangeAxis(), autoRangeIncludesZero)); createUI(createChartPanel(chart), createInputParameterPanel(), bindingContext); plot.getDomainAxis().addChangeListener(domainAxisChangeListener); scatterPlotDisplay.setMouseWheelEnabled(true); scatterPlotDisplay.setMouseZoomable(true); }
From source file:org.esa.beam.visat.toolviews.stat.ScatterPlotPanel.java
private void createUI() { final XYPlot plot = getPlot(); plot.setAxisOffset(new RectangleInsets(5, 5, 5, 5)); plot.setNoDataMessage(NO_DATA_MESSAGE); plot.setDataset(CONFIDENCE_DSINDEX, acceptableDeviationDataset); plot.setDataset(REGRESSION_DSINDEX, regressionDataset); plot.setDataset(SCATTERPOINTS_DSINDEX, scatterpointsDataset); plot.addAnnotation(r2Annotation); final DeviationRenderer identityRenderer = new DeviationRenderer(true, false); identityRenderer.setSeriesPaint(0, StatisticChartStyling.SAMPLE_DATA_PAINT); identityRenderer.setSeriesFillPaint(0, StatisticChartStyling.SAMPLE_DATA_FILL_PAINT); plot.setRenderer(CONFIDENCE_DSINDEX, identityRenderer); final DeviationRenderer regressionRenderer = new DeviationRenderer(true, false); regressionRenderer.setSeriesPaint(0, StatisticChartStyling.REGRESSION_DATA_PAINT); regressionRenderer.setSeriesFillPaint(0, StatisticChartStyling.REGRESSION_DATA_FILL_PAINT); plot.setRenderer(REGRESSION_DSINDEX, regressionRenderer); final XYErrorRenderer scatterPointsRenderer = new XYErrorRenderer(); scatterPointsRenderer.setDrawXError(true); scatterPointsRenderer.setErrorStroke(new BasicStroke(1)); scatterPointsRenderer.setErrorPaint(StatisticChartStyling.CORRELATIVE_POINT_OUTLINE_PAINT); scatterPointsRenderer.setSeriesShape(0, StatisticChartStyling.CORRELATIVE_POINT_SHAPE); scatterPointsRenderer.setSeriesOutlinePaint(0, StatisticChartStyling.CORRELATIVE_POINT_OUTLINE_PAINT); scatterPointsRenderer.setSeriesFillPaint(0, StatisticChartStyling.CORRELATIVE_POINT_FILL_PAINT); scatterPointsRenderer.setSeriesLinesVisible(0, false); scatterPointsRenderer.setSeriesShapesVisible(0, true); scatterPointsRenderer.setSeriesOutlineStroke(0, new BasicStroke(1.0f)); scatterPointsRenderer.setSeriesToolTipGenerator(0, new XYToolTipGenerator() { @Override/* w w w .ja v a 2s . co m*/ public String generateToolTip(XYDataset dataset, int series, int item) { final XYIntervalSeriesCollection collection = (XYIntervalSeriesCollection) dataset; final Comparable key = collection.getSeriesKey(series); final double xValue = collection.getXValue(series, item); final double endYValue = collection.getEndYValue(series, item); final double yValue = collection.getYValue(series, item); return String.format("%s: mean = %6.2f, sigma = %6.2f | %s: value = %6.2f", getRasterName(), yValue, endYValue - yValue, key, xValue); } }); plot.setRenderer(SCATTERPOINTS_DSINDEX, scatterPointsRenderer); final boolean autoRangeIncludesZero = false; final boolean xLog = scatterPlotModel.xAxisLogScaled; final boolean yLog = scatterPlotModel.yAxisLogScaled; plot.setDomainAxis( StatisticChartStyling.updateScalingOfAxis(xLog, plot.getDomainAxis(), autoRangeIncludesZero)); plot.setRangeAxis( StatisticChartStyling.updateScalingOfAxis(yLog, plot.getRangeAxis(), autoRangeIncludesZero)); createUI(createChartPanel(chart), createInputParameterPanel(), bindingContext); plot.getDomainAxis().addChangeListener(domainAxisChangeListener); scatterPlotDisplay.setMouseWheelEnabled(true); scatterPlotDisplay.setMouseZoomable(true); }