Examples with ChartOptions org.baderlab.csplugins.enrichmentmap.style.ChartOptions used on opensource projects

Example 1 with ChartOptions

use of org.baderlab.csplugins.enrichmentmap.style.ChartOptions in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method createStyleOptions.

private EMStyleOptions createStyleOptions(EnrichmentMap map, EMViewControlPanel viewPanel) {
    if (map == null || viewPanel == null)
        return null;
    Set<AbstractDataSet> dataSets = viewPanel.getDataSetSelector().getCheckedItems();
    boolean publicationReady = viewPanel.getPublicationReadyCheck().isSelected();
    boolean postAnalysis = map.hasSignatureDataSets();
    ChartData data = (ChartData) viewPanel.getChartDataCombo().getSelectedItem();
    ChartType type = getChartType(viewPanel);
    ColorScheme colorScheme = (ColorScheme) viewPanel.getChartColorsCombo().getSelectedItem();
    boolean showLabels = viewPanel.getShowChartLabelsCheck().isSelected();
    ChartOptions chartOptions = new ChartOptions(data, type, colorScheme, showLabels);
    return new EMStyleOptions(viewPanel.getNetworkView(), map, dataSets::contains, chartOptions, postAnalysis, publicationReady);
}

Example 2 with ChartOptions

use of org.baderlab.csplugins.enrichmentmap.style.ChartOptions in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method createChart.

public CyCustomGraphics2<?> createChart(EMStyleOptions options) {
    CyCustomGraphics2<?> chart = null;
    ChartOptions chartOptions = options.getChartOptions();
    ChartData data = chartOptions != null ? chartOptions.getData() : null;
    if (data != null && data != ChartData.NONE) {
        // Ignore Signature Data Sets in charts
        Set<EMDataSet> dataSets = filterDataSets(options.getDataSets());
        if (dataSets.size() > 1) {
            ColumnDescriptor<Double> columnDescriptor = data.getColumnDescriptor();
            List<CyColumnIdentifier> columns = ChartUtil.getSortedColumnIdentifiers(options.getAttributePrefix(), dataSets, columnDescriptor, columnIdFactory);
            ChartType type = chartOptions.getType();
            Map<String, Object> props = new HashMap<>(type.getProperties());
            props.put("cy_dataColumns", columns);
            List<Double> range = ChartUtil.calculateGlobalRange(options.getNetworkView().getModel(), columns);
            props.put("cy_range", range);
            props.put("cy_autoRange", false);
            props.put("cy_globalRange", true);
            props.put("cy_showItemLabels", chartOptions.isShowLabels());
            props.put("cy_colors", chartOptions.getColorScheme().getColors());
            try {
                CyCustomGraphics2Factory<?> factory = chartFactoryManager.getChartFactory(type.getId());
                if (factory != null)
                    chart = factory.getInstance(props);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    }
    return chart;
}

Example 3 with ChartOptions

use of org.baderlab.csplugins.enrichmentmap.style.ChartOptions in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method reset.

public void reset(ViewParams params) {
    long netViewID = params.getNetworkViewID();
    invokeOnEDT(() -> {
        EMViewControlPanel viewPanel = getControlPanel().getViewControlPanel(netViewID);
        if (viewPanel == null)
            return;
        EnrichmentMap map = emManager.getEnrichmentMap(viewPanel.getNetworkView().getModel().getSUID());
        if (map == null)
            return;
        try {
            // Update Filters
            if (params.getPValue() != null && viewPanel.getPValueSliderPanel() != null)
                viewPanel.getPValueSliderPanel().setValue(params.getPValue());
            if (params.getQValue() != null && viewPanel.getQValueSliderPanel() != null)
                viewPanel.getQValueSliderPanel().setValue(params.getQValue());
            if (params.getSimilarityCoefficient() != null && viewPanel.getSimilaritySliderPanel() != null)
                viewPanel.getSimilaritySliderPanel().setValue(params.getSimilarityCoefficient());
            if (params.getNodeCutoffParam() == CutoffParam.P_VALUE)
                viewPanel.getPValueRadio().doClick();
            else if (params.getNodeCutoffParam() == CutoffParam.Q_VALUE)
                viewPanel.getQValueRadio().doClick();
            Set<String> filteredOutDataSetNames = params.getFilteredOutDataSets();
            if (filteredOutDataSetNames != null && !filteredOutDataSetNames.isEmpty()) {
                Set<AbstractDataSet> allDataSets = viewPanel.getAllDataSets();
                Set<AbstractDataSet> filteredDataSets = allDataSets.stream().filter(ds -> !filteredOutDataSetNames.contains(ds.getName())).collect(Collectors.toSet());
                viewPanel.getDataSetSelector().setCheckedItems(filteredDataSets);
            }
            // Update Style options
            ChartOptions chartOptions = params.getChartOptions();
            viewPanel.getChartDataCombo().setSelectedItem(chartOptions != null ? chartOptions.getData() : null);
            viewPanel.getChartTypeCombo().setSelectedItem(chartOptions != null ? chartOptions.getType() : null);
            viewPanel.getChartColorsCombo().setSelectedItem(chartOptions != null ? chartOptions.getColorScheme() : null);
            viewPanel.getShowChartLabelsCheck().setSelected(chartOptions != null && chartOptions.isShowLabels());
            viewPanel.getPublicationReadyCheck().setSelected(params.isPublicationReady());
            viewPanel.updateChartDataCombo();
            updateVisualStyle(map, viewPanel);
            filterNodesAndEdges(viewPanel, map);
        } finally {
            updating = false;
        }
    });
}