Examples with EMDataSet org.baderlab.csplugins.enrichmentmap.model.EMDataSet used on opensource projects

Example 56 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class ModelSerializer method deserialize.

public static EnrichmentMap deserialize(String json) {
    Type immutableIntSetType = new TypeToken<ImmutableSet<Integer>>() {
    }.getType();
    Gson gson = new GsonBuilder().registerTypeAdapter(BiMap.class, new BiMapAdapter()).registerTypeHierarchyAdapter(Path.class, new PathAdapter()).registerTypeAdapter(EnrichmentResult.class, new EnrichmentResultAdapter()).registerTypeAdapter(immutableIntSetType, new ImmutableIntSetAdapter()).create();
    try {
        EnrichmentMap map = gson.fromJson(json, EnrichmentMap.class);
        for (EMDataSet dataset : map.getDataSetList()) {
            dataset.setParent(map);
        }
        return map;
    } catch (JsonParseException e) {
        logger.error(e.getMessage(), e);
        return null;
    }
}

Example 57 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class ChartUtil method createRadialHeatMapLegend.

public static JFreeChart createRadialHeatMapLegend(List<EMDataSet> dataSets, ChartOptions options) {
    // All the slices must have the same size
    final DefaultPieDataset pieDataset = new DefaultPieDataset();
    for (EMDataSet ds : dataSets) pieDataset.setValue(ds.getName(), 1);
    JFreeChart chart = ChartFactory.createPieChart(// chart title
    null, // data
    pieDataset, // include legend
    false, // tooltips
    true, // urls
    false);
    chart.setAntiAlias(true);
    chart.setBorderVisible(false);
    chart.setBackgroundPaint(UIManager.getColor("Table.background"));
    chart.setBackgroundImageAlpha(0.0f);
    chart.setPadding(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    final PiePlot plot = (PiePlot) chart.getPlot();
    plot.setCircular(true);
    plot.setOutlineVisible(false);
    plot.setBackgroundPaint(UIManager.getColor("Table.background"));
    plot.setInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setShadowPaint(TRANSPARENT_COLOR);
    plot.setShadowXOffset(0.0);
    plot.setShadowYOffset(0.0);
    plot.setLabelGenerator(new StandardPieSectionLabelGenerator("{0}"));
    plot.setLabelFont(UIManager.getFont("Label.font").deriveFont(LookAndFeelUtil.getSmallFontSize()));
    plot.setLabelPaint(UIManager.getColor("Label.foreground"));
    plot.setLabelBackgroundPaint(TRANSPARENT_COLOR);
    plot.setLabelOutlinePaint(TRANSPARENT_COLOR);
    plot.setLabelShadowPaint(TRANSPARENT_COLOR);
    plot.setToolTipGenerator(new StandardPieToolTipGenerator("{0}"));
    ColorScheme colorScheme = options != null ? options.getColorScheme() : null;
    List<Color> colors = colorScheme != null ? colorScheme.getColors() : null;
    if (// UP, ZERO, DOWN:
    colors == null || colors.size() < 3)
        colors = Arrays.asList(new Color[] { Color.LIGHT_GRAY, Color.WHITE, Color.DARK_GRAY });
    int total = dataSets.size();
    int v = total / -2;
    for (EMDataSet ds : dataSets) {
        plot.setSectionPaint(ds.getName(), ColorUtil.getColor(v, -total, total, colors.get(2), colors.get(1), colors.get(0)));
        v++;
    }
    return chart;
}

Example 58 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class ChartUtil method createHeatMapLegend.

@SuppressWarnings("serial")
public static JFreeChart createHeatMapLegend(List<EMDataSet> dataSets, ChartOptions options) {
    final DefaultCategoryDataset dataset = new DefaultCategoryDataset();
    for (EMDataSet ds : dataSets) dataset.addValue(1, options.getData().toString(), ds.getName());
    final JFreeChart chart = ChartFactory.createBarChart(// chart title
    null, // domain axis label
    null, // range axis label
    null, // data
    dataset, PlotOrientation.HORIZONTAL, // include legend
    false, // tooltips
    true, // urls
    false);
    chart.setAntiAlias(true);
    chart.setBorderVisible(false);
    chart.setBackgroundPaint(UIManager.getColor("Table.background"));
    chart.setBackgroundImageAlpha(0.0f);
    chart.setPadding(new RectangleInsets(0.0, 0.0, 0.0, 20.0));
    final CategoryPlot plot = (CategoryPlot) chart.getPlot();
    plot.setOutlineVisible(false);
    plot.setBackgroundPaint(UIManager.getColor("Table.background"));
    plot.setInsets(new RectangleInsets(0.0, 0.0, 0.0, 0.0));
    plot.setDomainGridlinesVisible(false);
    plot.setRangeGridlinesVisible(false);
    final CategoryAxis domainAxis = (CategoryAxis) plot.getDomainAxis();
    domainAxis.setVisible(true);
    domainAxis.setAxisLineVisible(false);
    domainAxis.setTickMarksVisible(false);
    domainAxis.setTickLabelFont(UIManager.getFont("Label.font").deriveFont(LookAndFeelUtil.getSmallFontSize()));
    domainAxis.setTickLabelPaint(UIManager.getColor("Label.foreground"));
    domainAxis.setTickLabelInsets(new RectangleInsets(0.0, 0.0, 0.0, 15.0));
    domainAxis.setCategoryMargin(0.0);
    final NumberAxis rangeAxis = (NumberAxis) plot.getRangeAxis();
    rangeAxis.setVisible(false);
    ColorScheme colorScheme = options != null ? options.getColorScheme() : null;
    List<Color> colors = colorScheme != null ? colorScheme.getColors() : null;
    if (// UP, ZERO, DOWN:
    colors == null || colors.size() < 3)
        colors = Arrays.asList(new Color[] { Color.LIGHT_GRAY, Color.WHITE, Color.DARK_GRAY });
    List<Color> itemColors = new ArrayList<>();
    int total = dataSets.size();
    int v = total / 2;
    for (int i = 0; i < total; i++) itemColors.add(ColorUtil.getColor(v--, -total, total, colors.get(2), colors.get(1), colors.get(0)));
    final BarRenderer renderer = new BarRenderer() {

        @Override
        public Paint getItemPaint(int row, int column) {
            return column < itemColors.size() ? itemColors.get(column) : Color.LIGHT_GRAY;
        }
    };
    plot.setRenderer(renderer);
    renderer.setBarPainter(new StandardBarPainter());
    renderer.setDrawBarOutline(true);
    renderer.setShadowVisible(false);
    renderer.setItemMargin(0.0);
    renderer.setBaseToolTipGenerator(new StandardCategoryToolTipGenerator("{1}", NumberFormat.getInstance()));
    return chart;
}