List of usage examples for java.awt Color getHSBColor
public static Color getHSBColor(float h, float s, float b)
From source file:gate.gui.docview.AnnotationStack.java
/** * Draw the annotation stack in a JPanel with a GridBagLayout. *///from w w w. j a va 2 s.c om public void drawStack() { // clear the panel removeAll(); boolean textTooLong = text.length() > maxTextLength; int upperBound = text.length() - (maxTextLength / 2); GridBagConstraints gbc = new GridBagConstraints(); gbc.gridx = 0; gbc.gridy = 0; gbc.fill = GridBagConstraints.BOTH; /********************** * First row of text * *********************/ gbc.gridwidth = 1; gbc.insets = new java.awt.Insets(10, 10, 10, 10); JLabel labelTitle = new JLabel("Context"); labelTitle.setOpaque(true); labelTitle.setBackground(Color.WHITE); labelTitle.setBorder(new CompoundBorder( new EtchedBorder(EtchedBorder.LOWERED, new Color(250, 250, 250), new Color(250, 250, 250).darker()), new EmptyBorder(new Insets(0, 2, 0, 2)))); labelTitle.setToolTipText("Expression and its context."); add(labelTitle, gbc); gbc.insets = new java.awt.Insets(10, 0, 10, 0); int expressionStart = contextBeforeSize; int expressionEnd = text.length() - contextAfterSize; // for each character for (int charNum = 0; charNum < text.length(); charNum++) { gbc.gridx = charNum + 1; if (textTooLong) { if (charNum == maxTextLength / 2) { // add ellipsis dots in case of a too long text displayed add(new JLabel("..."), gbc); // skip the middle part of the text if too long charNum = upperBound + 1; continue; } else if (charNum > upperBound) { gbc.gridx -= upperBound - (maxTextLength / 2) + 1; } } // set the text and color of the feature value JLabel label = new JLabel(text.substring(charNum, charNum + 1)); if (charNum >= expressionStart && charNum < expressionEnd) { // this part is matched by the pattern, color it label.setBackground(new Color(240, 201, 184)); } else { // this part is the context, no color label.setBackground(Color.WHITE); } label.setOpaque(true); // get the word from which belongs the current character charNum int start = text.lastIndexOf(" ", charNum); int end = text.indexOf(" ", charNum); String word = text.substring((start == -1) ? 0 : start, (end == -1) ? text.length() : end); // add a mouse listener that modify the query label.addMouseListener(textMouseListener.createListener(word)); add(label, gbc); } /************************************ * Subsequent rows with annotations * ************************************/ // for each row to display for (StackRow stackRow : stackRows) { String type = stackRow.getType(); String feature = stackRow.getFeature(); if (feature == null) { feature = ""; } String shortcut = stackRow.getShortcut(); if (shortcut == null) { shortcut = ""; } gbc.gridy++; gbc.gridx = 0; gbc.gridwidth = 1; gbc.insets = new Insets(0, 0, 3, 0); // add the header of the row JLabel annotationTypeAndFeature = new JLabel(); String typeAndFeature = type + (feature.equals("") ? "" : ".") + feature; annotationTypeAndFeature.setText(!shortcut.equals("") ? shortcut : stackRow.getSet() != null ? stackRow.getSet() + "#" + typeAndFeature : typeAndFeature); annotationTypeAndFeature.setOpaque(true); annotationTypeAndFeature.setBackground(Color.WHITE); annotationTypeAndFeature .setBorder(new CompoundBorder(new EtchedBorder(EtchedBorder.LOWERED, new Color(250, 250, 250), new Color(250, 250, 250).darker()), new EmptyBorder(new Insets(0, 2, 0, 2)))); if (feature.equals("")) { annotationTypeAndFeature.addMouseListener(headerMouseListener.createListener(type)); } else { annotationTypeAndFeature.addMouseListener(headerMouseListener.createListener(type, feature)); } gbc.insets = new java.awt.Insets(0, 10, 3, 10); add(annotationTypeAndFeature, gbc); gbc.insets = new java.awt.Insets(0, 0, 3, 0); // add all annotations for this row HashMap<Integer, TreeSet<Integer>> gridSet = new HashMap<Integer, TreeSet<Integer>>(); int gridyMax = gbc.gridy; for (StackAnnotation ann : stackRow.getAnnotations()) { gbc.gridx = ann.getStartNode().getOffset().intValue() - expressionStartOffset + contextBeforeSize + 1; gbc.gridwidth = ann.getEndNode().getOffset().intValue() - ann.getStartNode().getOffset().intValue(); if (gbc.gridx == 0) { // column 0 is already the row header gbc.gridwidth -= 1; gbc.gridx = 1; } else if (gbc.gridx < 0) { // annotation starts before displayed text gbc.gridwidth += gbc.gridx - 1; gbc.gridx = 1; } if (gbc.gridx + gbc.gridwidth > text.length()) { // annotation ends after displayed text gbc.gridwidth = text.length() - gbc.gridx + 1; } if (textTooLong) { if (gbc.gridx > (upperBound + 1)) { // x starts after the hidden middle part gbc.gridx -= upperBound - (maxTextLength / 2) + 1; } else if (gbc.gridx > (maxTextLength / 2)) { // x starts in the hidden middle part if (gbc.gridx + gbc.gridwidth <= (upperBound + 3)) { // x ends in the hidden middle part continue; // skip the middle part of the text } else { // x ends after the hidden middle part gbc.gridwidth -= upperBound - gbc.gridx + 2; gbc.gridx = (maxTextLength / 2) + 2; } } else { // x starts before the hidden middle part if (gbc.gridx + gbc.gridwidth < (maxTextLength / 2)) { // x ends before the hidden middle part // do nothing } else if (gbc.gridx + gbc.gridwidth < upperBound) { // x ends in the hidden middle part gbc.gridwidth = (maxTextLength / 2) - gbc.gridx + 1; } else { // x ends after the hidden middle part gbc.gridwidth -= upperBound - (maxTextLength / 2) + 1; } } } if (gbc.gridwidth == 0) { gbc.gridwidth = 1; } JLabel label = new JLabel(); Object object = ann.getFeatures().get(feature); String value = (object == null) ? " " : Strings.toString(object); if (value.length() > maxFeatureValueLength) { // show the full text in the tooltip label.setToolTipText((value.length() > 500) ? "<html><textarea rows=\"30\" cols=\"40\" readonly=\"readonly\">" + value.replaceAll("(.{50,60})\\b", "$1\n") + "</textarea></html>" : ((value.length() > 100) ? "<html><table width=\"500\" border=\"0\" cellspacing=\"0\">" + "<tr><td>" + value.replaceAll("\n", "<br>") + "</td></tr></table></html>" : value)); if (stackRow.getCrop() == CROP_START) { value = "..." + value.substring(value.length() - maxFeatureValueLength - 1); } else if (stackRow.getCrop() == CROP_END) { value = value.substring(0, maxFeatureValueLength - 2) + "..."; } else {// cut in the middle value = value.substring(0, maxFeatureValueLength / 2) + "..." + value.substring(value.length() - (maxFeatureValueLength / 2)); } } label.setText(value); label.setBackground(AnnotationSetsView.getColor(stackRow.getSet(), ann.getType())); label.setBorder(BorderFactory.createLineBorder(Color.BLACK, 1)); label.setOpaque(true); label.addMouseListener(annotationMouseListener.createListener(stackRow.getSet(), type, String.valueOf(ann.getId()))); // show the feature values in the tooltip if (!ann.getFeatures().isEmpty()) { String width = (Strings.toString(ann.getFeatures()).length() > 100) ? "500" : "100%"; String toolTip = "<html><table width=\"" + width + "\" border=\"0\" cellspacing=\"0\" cellpadding=\"4\">"; Color color = (Color) UIManager.get("ToolTip.background"); float[] hsb = Color.RGBtoHSB(color.getRed(), color.getGreen(), color.getBlue(), null); color = Color.getHSBColor(hsb[0], hsb[1], Math.max(0f, hsb[2] - hsb[2] * 0.075f)); // darken the color String hexColor = Integer.toHexString(color.getRed()) + Integer.toHexString(color.getGreen()) + Integer.toHexString(color.getBlue()); boolean odd = false; // alternate background color every other row List<Object> features = new ArrayList<Object>(ann.getFeatures().keySet()); //sort the features into alphabetical order Collections.sort(features, new Comparator<Object>() { @Override public int compare(Object o1, Object o2) { return o1.toString().compareToIgnoreCase(o2.toString()); } }); for (Object key : features) { String fv = Strings.toString(ann.getFeatures().get(key)); toolTip += "<tr align=\"left\"" + (odd ? " bgcolor=\"#" + hexColor + "\"" : "") + "><td><strong>" + key + "</strong></td><td>" + ((fv.length() > 500) ? "<textarea rows=\"20\" cols=\"40\" cellspacing=\"0\">" + StringEscapeUtils .escapeHtml(fv.replaceAll("(.{50,60})\\b", "$1\n")) + "</textarea>" : StringEscapeUtils.escapeHtml(fv).replaceAll("\n", "<br>")) + "</td></tr>"; odd = !odd; } label.setToolTipText(toolTip + "</table></html>"); } else { label.setToolTipText("No features."); } if (!feature.equals("")) { label.addMouseListener(annotationMouseListener.createListener(stackRow.getSet(), type, feature, Strings.toString(ann.getFeatures().get(feature)), String.valueOf(ann.getId()))); } // find the first empty row span for this annotation int oldGridy = gbc.gridy; for (int y = oldGridy; y <= (gridyMax + 1); y++) { // for each cell of this row where spans the annotation boolean xSpanIsEmpty = true; for (int x = gbc.gridx; (x < (gbc.gridx + gbc.gridwidth)) && xSpanIsEmpty; x++) { xSpanIsEmpty = !(gridSet.containsKey(x) && gridSet.get(x).contains(y)); } if (xSpanIsEmpty) { gbc.gridy = y; break; } } // save the column x and row y of the current value TreeSet<Integer> ts; for (int x = gbc.gridx; x < (gbc.gridx + gbc.gridwidth); x++) { ts = gridSet.get(x); if (ts == null) { ts = new TreeSet<Integer>(); } ts.add(gbc.gridy); gridSet.put(x, ts); } add(label, gbc); gridyMax = Math.max(gridyMax, gbc.gridy); gbc.gridy = oldGridy; } // add a button at the end of the row gbc.gridwidth = 1; if (stackRow.getLastColumnButton() != null) { // last cell of the row gbc.gridx = Math.min(text.length(), maxTextLength) + 1; gbc.insets = new Insets(0, 10, 3, 0); gbc.fill = GridBagConstraints.NONE; gbc.anchor = GridBagConstraints.WEST; add(stackRow.getLastColumnButton(), gbc); gbc.insets = new Insets(0, 0, 3, 0); gbc.fill = GridBagConstraints.BOTH; gbc.anchor = GridBagConstraints.CENTER; } // set the new gridy to the maximum row we put a value gbc.gridy = gridyMax; } if (lastRowButton != null) { // add a configuration button on the last row gbc.insets = new java.awt.Insets(0, 10, 0, 10); gbc.gridx = 0; gbc.gridy++; add(lastRowButton, gbc); } // add an empty cell that takes all remaining space to // align the visible cells at the top-left corner gbc.gridy++; gbc.gridx = Math.min(text.length(), maxTextLength) + 1; gbc.gridwidth = GridBagConstraints.REMAINDER; gbc.gridheight = GridBagConstraints.REMAINDER; gbc.weightx = 1; gbc.weighty = 1; add(new JLabel(""), gbc); validate(); updateUI(); }
From source file:Interface.Caruser.Pendingrequest.java
public void populatetable() { DefaultTableModel model = (DefaultTableModel) incomingjTable.getModel(); model.setRowCount(0);//from w w w .ja va 2s . co m for (WorkRequest request : organization.getWorkQueue().getWorkRequestList()) { Object[] row = new Object[7]; row[0] = request; row[1] = request.getSender(); row[2] = request.getReceiver(); row[3] = request.getSource(); row[4] = request.getDestination(); Format formatter = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss"); row[5] = formatter.format(request.getRequestDate()); row[6] = request.getStatus(); model.addRow(row); } incomingjTable.setSelectionBackground(Color.getHSBColor(0.2F, 0.1F, 0.2F)); incomingjTable.setSelectionForeground(Color.white); }
From source file:ala.soils2sat.DrawingUtils.java
public static List<Color> generatePalette(int size, Color baseColor) { float[] hsb = { 0, 0, 0 }; Color.RGBtoHSB(baseColor.getRed(), baseColor.getGreen(), baseColor.getBlue(), hsb); double baseHue = hsb[0]; List<Color> colors = new ArrayList<Color>(); colors.add(baseColor);//from w w w . ja v a 2s. c o m double step = (240.0 / (double) size); for (int i = 1; i < size; ++i) { float hue = (float) ((baseHue + step * ((double) i)) % 240.0); // this gives a number out of 240. need to scale that to percent hue = hue / 240; Color nextColor = Color.getHSBColor(hue, hsb[1], hsb[2]); colors.add(nextColor); } return colors; }
From source file:GeMSE.GS.Analysis.Stats.OneSamplePCAPanel.java
private void Plot() { double[][] data = _principalComponents.getData(); if (data[0].length < 2) { JOptionPane.showMessageDialog(this, "An error occured when computing principal components. " + "\nRequire at least two principal components, but calculated " + String.valueOf(data[0].length) + "\n", "Not enough data", JOptionPane.ERROR_MESSAGE); return;// w w w .j av a 2 s . c o m } float[] yAxisColor = new float[3]; Color.RGBtoHSB(255, 255, 255, yAxisColor); float[] hsbValues = new float[3]; Color.RGBtoHSB(16, 23, 67, hsbValues); float[] pcColor = new float[3]; Color.RGBtoHSB(255, 255, 0, pcColor); XYSeriesCollection dataset = new XYSeriesCollection(); XYSeries series = new XYSeries("PC"); for (double[] d : data) series.add(d[0], d[1]); dataset.addSeries(series); JFreeChart chart = ChartFactory.createScatterPlot(null, "Principal component 1", "Principal component 2", (XYDataset) dataset); chart.setBackgroundPaint(Color.getHSBColor(hsbValues[0], hsbValues[1], hsbValues[2])); chart.removeLegend(); XYPlot plot = (XYPlot) chart.getPlot(); plot.setBackgroundPaint(Color.getHSBColor(hsbValues[0], hsbValues[1], hsbValues[2])); Font axisLabelFont = new Font("Dialog", Font.PLAIN, 14); Font axisTickLabelFont = new Font("Dialog", Font.PLAIN, 12); plot.setDomainGridlinePaint(Color.gray); plot.setRangeGridlinePaint(Color.gray); plot.getDomainAxis().setTickLabelPaint(Color.white); plot.getDomainAxis().setLabelPaint(Color.white); plot.getDomainAxis().setLabelFont(axisLabelFont); plot.getDomainAxis().setTickLabelFont(axisTickLabelFont); plot.getRangeAxis().setTickLabelPaint(Color.getHSBColor(yAxisColor[0], yAxisColor[1], yAxisColor[2])); plot.getRangeAxis().setLabelPaint(Color.getHSBColor(yAxisColor[0], yAxisColor[1], yAxisColor[2])); plot.getRangeAxis().setLabelFont(axisLabelFont); plot.getRangeAxis().setTickLabelFont(axisTickLabelFont); Shape shape = ShapeUtilities.createDiagonalCross(4, 0.5f); XYItemRenderer renderer = chart.getXYPlot().getRenderer(); renderer.setSeriesShape(0, shape); renderer.setSeriesPaint(0, Color.getHSBColor(pcColor[0], pcColor[1], pcColor[2])); ChartPanel panel = new ChartPanel(chart); Dimension plotDim = plotPanel.getSize(); plotDim.height -= (plotDim.height * 10) / 100; plotDim.width -= (plotDim.width * 10) / 100; panel.setPreferredSize(plotDim); plotPanel.setViewportView(panel); revalidate(); repaint(); }
From source file:org.gwaspi.gui.reports.SampleQAHetzygPlotZoom.java
private JFreeChart createChart(XYDataset dataset) { JFreeChart chart = ChartFactory.createScatterPlot("Heterozygosity vs. Missing Ratio", "Heterozygosity Ratio", "Missing Ratio", dataset, PlotOrientation.VERTICAL, true, false, false); 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(PLOT_MANHATTAN_BACKGROUND); // Hue, saturation, brightness 9 // GRIDLINES/*from w w w . j a v a2 s .c o m*/ plot.setDomainGridlineStroke(new BasicStroke(0.0f)); plot.setDomainMinorGridlineStroke(new BasicStroke(0.0f)); plot.setDomainGridlinePaint(PLOT_MANHATTAN_BACKGROUND.darker().darker()); // Hue, saturation, brightness 7 plot.setDomainMinorGridlinePaint(PLOT_MANHATTAN_BACKGROUND); // Hue, saturation, brightness 9 plot.setRangeGridlineStroke(new BasicStroke(0.0f)); plot.setRangeMinorGridlineStroke(new BasicStroke(0.0f)); plot.setRangeGridlinePaint(PLOT_MANHATTAN_BACKGROUND.darker().darker()); // Hue, saturation, brightness 7 plot.setRangeMinorGridlinePaint(PLOT_MANHATTAN_BACKGROUND.darker()); // Hue, saturation, brightness 8 plot.setDomainMinorGridlinesVisible(true); plot.setRangeMinorGridlinesVisible(true); // DOTS RENDERER XYLineAndShapeRenderer renderer = (XYLineAndShapeRenderer) plot.getRenderer(); renderer.setSeriesPaint(0, PLOT_MANHATTAN_DOTS); // renderer.setSeriesOutlinePaint(0, Color.DARK_GRAY); // renderer.setUseOutlinePaint(true); // Set dot shape of the currently appended Series renderer.setSeriesShape(0, new Rectangle2D.Double(-1, -1, 2, 2)); renderer.setSeriesVisibleInLegend(0, false); // AXIS double maxHetzy = 0.005; for (int i = 0; i < dataset.getItemCount(0); i++) { if (maxHetzy < dataset.getXValue(0, i)) { maxHetzy = dataset.getXValue(0, i); } } NumberAxis hetzyAxis = (NumberAxis) plot.getDomainAxis(); hetzyAxis.setAutoRangeIncludesZero(true); hetzyAxis.setAxisLineVisible(true); hetzyAxis.setTickLabelsVisible(true); hetzyAxis.setTickMarksVisible(true); hetzyAxis.setRange(0, maxHetzy * 1.1); double maxMissrat = 0.005; for (int i = 0; i < dataset.getItemCount(0); i++) { if (maxMissrat < dataset.getYValue(0, i)) { maxMissrat = dataset.getYValue(0, i); } } NumberAxis missratAxis = (NumberAxis) plot.getRangeAxis(); missratAxis.setAutoRangeIncludesZero(true); missratAxis.setAxisLineVisible(true); missratAxis.setTickLabelsVisible(true); missratAxis.setTickMarksVisible(true); missratAxis.setRange(0, maxMissrat * 1.1); // Add significance Threshold to subplot final Marker missingThresholdLine = new ValueMarker(missingThreshold); missingThresholdLine.setPaint(Color.blue); final Marker hetzyThresholdLine = new ValueMarker(hetzyThreshold); hetzyThresholdLine.setPaint(Color.blue); // Add legend to hetzyThreshold hetzyThresholdLine.setLabel("hetzyg. threshold = " + hetzyThreshold); missingThresholdLine.setLabel("missing. threshold = " + missingThreshold); hetzyThresholdLine.setLabelAnchor(RectangleAnchor.TOP_LEFT); hetzyThresholdLine.setLabelTextAnchor(TextAnchor.TOP_RIGHT); missingThresholdLine.setLabelAnchor(RectangleAnchor.BOTTOM_LEFT); missingThresholdLine.setLabelTextAnchor(TextAnchor.TOP_LEFT); plot.addRangeMarker(missingThresholdLine); // THIS FOR MISSING RATIO plot.addDomainMarker(hetzyThresholdLine); // THIS FOR HETZY RATIO // Marker label if below hetzyThreshold XYItemRenderer lblRenderer = plot.getRenderer(); // THRESHOLD AND SELECTED LABEL GENERATOR MySeriesItemLabelGenerator lblGenerator = new MySeriesItemLabelGenerator(hetzyThreshold, missingThreshold); lblRenderer.setSeriesItemLabelGenerator(0, lblGenerator); lblRenderer.setSeriesItemLabelFont(0, new Font("SansSerif", Font.PLAIN, 10)); lblRenderer.setSeriesPositiveItemLabelPosition(0, new ItemLabelPosition(ItemLabelAnchor.CENTER, TextAnchor.BOTTOM_LEFT, TextAnchor.BOTTOM_LEFT, 2 * Math.PI)); // TOOLTIP GENERATOR MyXYToolTipGenerator tooltipGenerator = new MyXYToolTipGenerator(); lblRenderer.setBaseToolTipGenerator(tooltipGenerator); lblRenderer.setSeriesItemLabelsVisible(0, true); return chart; }
From source file:com.planetmayo.debrief.satc_rcp.views.SpatialView.java
public static Color[] getDifferentColors(int n) { Color[] cols = new Color[n]; for (int i = 0; i < n; i++) cols[i] = Color.getHSBColor((float) (n - i) / n, 1, 1); // return cols; return randomizeArray(cols); }
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 w w . jav a 2 s .com*/ 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: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; }/* w ww .ja v a 2 s .co m*/ 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; }
From source file:ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController.java
/** * Visualization of the correlation of principal components with factors or the date samples were run. * * @param svdo SVD value object/* w w w. j a va 2 s. c om*/ */ private void writePCAFactors(OutputStream os, ExpressionExperiment ee, SVDValueObject svdo) throws Exception { 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()); if (factorCorrelations.isEmpty() && dateCorrelations.isEmpty()) { this.writePlaceholderImage(os); return; } ee = expressionExperimentService.thawLite(ee); // need the experimental design int maxWidth = 10; Map<Long, String> efs = this.getFactorNames(ee, maxWidth); DefaultCategoryDataset series = new DefaultCategoryDataset(); /* * With two groups, or a continuous factor, we get rank correlations */ int MAX_COMP = 3; double STUB = 0.05; // always plot a little thing so we know its there. for (Integer component : factorCorrelations.keySet()) { if (component >= MAX_COMP) break; for (Long efId : factorCorrelations.get(component).keySet()) { Double a = factorCorrelations.get(component).get(efId); String facname = efs.get(efId) == null ? "?" : efs.get(efId); if (a != null && !Double.isNaN(a)) { Double corr = Math.max(STUB, Math.abs(a)); series.addValue(corr, "PC" + (component + 1), facname); } } } for (Integer component : dateCorrelations.keySet()) { if (component >= MAX_COMP) break; Double a = dateCorrelations.get(component); if (a != null && !Double.isNaN(a)) { Double corr = Math.max(STUB, Math.abs(a)); series.addValue(corr, "PC" + (component + 1), "Date run"); } } ChartFactory.setChartTheme(StandardChartTheme.createLegacyTheme()); JFreeChart chart = ChartFactory.createBarChart("", "Factors", "Component assoc.", series, PlotOrientation.VERTICAL, true, false, false); chart.getCategoryPlot().getRangeAxis().setRange(0, 1); BarRenderer renderer = (BarRenderer) chart.getCategoryPlot().getRenderer(); renderer.setBasePaint(Color.white); renderer.setShadowVisible(false); chart.getCategoryPlot().setRangeGridlinesVisible(false); chart.getCategoryPlot().setDomainGridlinesVisible(false); ChartUtilities.applyCurrentTheme(chart); CategoryAxis domainAxis = chart.getCategoryPlot().getDomainAxis(); domainAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_45); for (int i = 0; i < MAX_COMP; i++) { /* * Hue is straightforward; brightness is set medium to make it muted; saturation we vary from high to low. */ float saturationDrop = (float) Math.min(1.0, i * 1.3f / MAX_COMP); renderer.setSeriesPaint(i, Color.getHSBColor(0.0f, 1.0f - saturationDrop, 0.7f)); } /* * Give figure more room .. up to a limit */ int width = ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX; if (chart.getCategoryPlot().getCategories().size() > 3) { width = width + 40 * (chart.getCategoryPlot().getCategories().size() - 2); } int MAX_QC_IMAGE_SIZE_PX = 500; width = Math.min(width, MAX_QC_IMAGE_SIZE_PX); ChartUtilities.writeChartAsPNG(os, chart, width, ExpressionExperimentQCController.DEFAULT_QC_IMAGE_SIZE_PX); }
From source file:com.actelion.research.table.view.JVisualization.java
/** * Generates a neutral grey with given contrast to given color. * @param contrast 0.0 (not visible) to 1.0 (full contrast) * @return/* w w w . j av a 2 s. c o m*/ */ protected Color getContrastGrey(float contrast, Color color) { float brightness = ColorHelper.perceivedBrightness(color); float range = (brightness > 0.5) ? brightness : 1f - brightness; // enhance contrast for middle bright backgrounds contrast = (float) Math.pow(contrast, range); return (brightness > 0.5) ? Color.getHSBColor(0.0f, 0.0f, brightness - range * contrast) : Color.getHSBColor(0.0f, 0.0f, brightness + range * contrast); }