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chrtannuschrtannus
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Chart data now defaults to "NES" when all datasets are GSEA and "FDR" if there are other dataset methods (there must be at least 2 datasets).
1 parent b721085 commit a031dda

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2 files changed

+202
-161
lines changed

2 files changed

+202
-161
lines changed

‎EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/control/ControlPanelMediator.java‎

Lines changed: 198 additions & 160 deletions
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,7 @@
1818
import java.util.HashSet;
1919
import java.util.List;
2020
import java.util.Map;
21+
import java.util.Optional;
2122
import java.util.Properties;
2223
import java.util.Set;
2324
import java.util.concurrent.ForkJoinPool;
@@ -36,6 +37,7 @@
3637
import org.baderlab.csplugins.enrichmentmap.model.AbstractDataSet;
3738
import org.baderlab.csplugins.enrichmentmap.model.EMCreationParameters;
3839
import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
40+
import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
3941
import org.baderlab.csplugins.enrichmentmap.model.EMSignatureDataSet;
4042
import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
4143
import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
@@ -361,187 +363,223 @@ public void handleEvent(NetworkViewAboutToBeDestroyedEvent e) {
361363

362364
private void setCurrentNetworkView(CyNetworkView netView) {
363365
invokeOnEDT(() -> {
366+
EMViewControlPanel viewPanel = null;
364367
updating = true;
365368

366369
try {
367370
if (netView != null && !getControlPanel().contains(netView))
368-
addNetworkView(netView);
371+
viewPanel = addNetworkView(netView);
369372

370373
getControlPanel().update(netView);
371374
} finally {
372375
updating = false;
373376
}
377+
378+
if (viewPanel != null)
379+
setDefaults(viewPanel, emManager.getEnrichmentMap(netView.getModel().getSUID()));
374380
});
375381
}
376382

383+
/**
384+
* Call this method on the EDT only!
385+
*/
386+
private EMViewControlPanel addNetworkView(CyNetworkView netView) {
387+
EMViewControlPanel viewPanel = null;
388+
EnrichmentMap map = emManager.getEnrichmentMap(netView.getModel().getSUID());
389+
390+
// Is the new view an EnrichmentMap one?
391+
if (map != null) {
392+
viewPanel = getControlPanel().addEnrichmentMapView(netView);
393+
394+
if (viewPanel != null)
395+
addListeners(viewPanel, map);
396+
}
397+
398+
return viewPanel;
399+
}
400+
401+
/**
402+
* Add listeners to the new panel's fields.
403+
*/
377404
@SuppressWarnings("unchecked")
378-
private void addNetworkView(CyNetworkView netView) {
379-
invokeOnEDT(() -> {
380-
EnrichmentMap map = emManager.getEnrichmentMap(netView.getModel().getSUID());
405+
private void addListeners(EMViewControlPanel viewPanel, EnrichmentMap map) {
406+
CyNetworkView netView = viewPanel.getNetworkView();
407+
408+
viewPanel.getQValueRadio().addActionListener(evt -> {
409+
viewPanel.updateFilterPanel();
381410

382-
// Is the new view an EnrichmentMap one?
383-
if (map != null) {
384-
EMViewControlPanel viewPanel = getControlPanel().addEnrichmentMapView(netView);
385-
386-
if (viewPanel != null) {
387-
// Add listeners to the new panel's fields
388-
viewPanel.getQValueRadio().addActionListener(evt -> {
389-
viewPanel.updateFilterPanel();
390-
391-
if (!updating)
392-
filterNodesAndEdges(viewPanel, map);
393-
});
394-
viewPanel.getPValueRadio().addActionListener(evt -> {
395-
viewPanel.updateFilterPanel();
396-
397-
if (!updating)
398-
filterNodesAndEdges(viewPanel, map);
399-
});
400-
401-
SliderBarPanel pvSliderPanel = viewPanel.getPValueSliderPanel();
402-
SliderBarPanel qvSliderPanel = viewPanel.getQValueSliderPanel();
403-
SliderBarPanel sSliderPanel = viewPanel.getSimilaritySliderPanel();
404-
405-
if (pvSliderPanel != null)
406-
pvSliderPanel.addChangeListener(evt -> {
407-
if (!updating)
408-
filterNodesAndEdges(viewPanel, map);
409-
});
410-
if (qvSliderPanel != null)
411-
qvSliderPanel.addChangeListener(evt -> {
412-
if (!updating)
413-
filterNodesAndEdges(viewPanel, map);
414-
});
415-
if (sSliderPanel != null)
416-
sSliderPanel.addChangeListener(evt -> {
417-
if (!updating)
418-
filterNodesAndEdges(viewPanel, map);
419-
});
411+
if (!updating)
412+
filterNodesAndEdges(viewPanel, map);
413+
});
414+
viewPanel.getPValueRadio().addActionListener(evt -> {
415+
viewPanel.updateFilterPanel();
416+
417+
if (!updating)
418+
filterNodesAndEdges(viewPanel, map);
419+
});
420+
421+
SliderBarPanel pvSliderPanel = viewPanel.getPValueSliderPanel();
422+
SliderBarPanel qvSliderPanel = viewPanel.getQValueSliderPanel();
423+
SliderBarPanel sSliderPanel = viewPanel.getSimilaritySliderPanel();
424+
425+
if (pvSliderPanel != null)
426+
pvSliderPanel.addChangeListener(evt -> {
427+
if (!updating)
428+
filterNodesAndEdges(viewPanel, map);
429+
});
430+
if (qvSliderPanel != null)
431+
qvSliderPanel.addChangeListener(evt -> {
432+
if (!updating)
433+
filterNodesAndEdges(viewPanel, map);
434+
});
435+
if (sSliderPanel != null)
436+
sSliderPanel.addChangeListener(evt -> {
437+
if (!updating)
438+
filterNodesAndEdges(viewPanel, map);
439+
});
420440

421-
viewPanel.getDataSetSelector().addPropertyChangeListener("checkedData", evt -> {
422-
if (!updating) {
423-
viewPanel.updateChartDataCombo();
424-
425-
filterNodesAndEdges(viewPanel, map);
426-
ChartData data = (ChartData) viewPanel.getChartDataCombo().getSelectedItem();
427-
428-
Set<EMDataSet> oldDataSets = filterDataSets(
429-
(Collection<AbstractDataSet>) evt.getOldValue());
430-
Set<EMDataSet> newDataSets = filterDataSets(
431-
(Collection<AbstractDataSet>) evt.getNewValue());
432-
int oldSize = oldDataSets.size();
433-
int newSize = newDataSets.size();
434-
435-
// Cases where changing the number of checked datasets (Signatures excluded)
436-
// requires the style to be updated:
437-
// a) Chart data may change:
438-
boolean updateStyle = data != null && data != ChartData.NONE && oldSize != newSize;
439-
// b) Node color/shape may change:
440-
updateStyle = updateStyle || oldSize == 0 && newSize > 0;
441-
updateStyle = updateStyle || oldSize > 0 && newSize == 0;
442-
updateStyle = updateStyle || oldSize == 1 && newSize > 1;
443-
updateStyle = updateStyle || oldSize > 1 && newSize == 1;
441+
viewPanel.getDataSetSelector().addPropertyChangeListener("checkedData", evt -> {
442+
if (!updating) {
443+
viewPanel.updateChartDataCombo();
444+
445+
filterNodesAndEdges(viewPanel, map);
446+
ChartData data = (ChartData) viewPanel.getChartDataCombo().getSelectedItem();
447+
448+
Set<EMDataSet> oldDataSets = filterDataSets((Collection<AbstractDataSet>) evt.getOldValue());
449+
Set<EMDataSet> newDataSets = filterDataSets((Collection<AbstractDataSet>) evt.getNewValue());
450+
int oldSize = oldDataSets.size();
451+
int newSize = newDataSets.size();
452+
453+
// Cases where changing the number of checked datasets (Signatures excluded)
454+
// requires the style to be updated:
455+
// a) Chart data may change:
456+
boolean updateStyle = data != null && data != ChartData.NONE && oldSize != newSize;
457+
// b) Node color/shape may change:
458+
updateStyle = updateStyle || oldSize == 0 && newSize > 0;
459+
updateStyle = updateStyle || oldSize > 0 && newSize == 0;
460+
updateStyle = updateStyle || oldSize == 1 && newSize > 1;
461+
updateStyle = updateStyle || oldSize > 1 && newSize == 1;
444462

445-
if (updateStyle)
446-
updateVisualStyle(map, viewPanel);
447-
else
448-
netView.updateView();
449-
}
450-
});
451-
452-
viewPanel.getDataSetSelector().getAddButton().addActionListener(evt -> {
453-
postAnalysisPanelMediatorProvider.get().showDialog(viewPanel, netView);
454-
});
455-
viewPanel.getDataSetSelector().getTable().addMouseListener(new MouseAdapter() {
456-
@Override
457-
public void mousePressed(final MouseEvent e) {
458-
maybeShowContextMenu(e);
459-
}
460-
@Override
461-
public void mouseReleased(final MouseEvent e) {
462-
maybeShowContextMenu(e);
463-
}
464-
private void maybeShowContextMenu(final MouseEvent e) {
465-
if (e.isPopupTrigger()) {
466-
final JPopupMenu contextMenu = new JPopupMenu();
467-
{
468-
JMenuItem mi = new JMenuItem("Select nodes and edges from selected data sets");
469-
mi.addActionListener(evt -> selectNodesEdges(viewPanel.getNetworkView(),
470-
viewPanel.getDataSetSelector().getSelectedItems()));
471-
contextMenu.add(mi);
472-
}
473-
contextMenu.addSeparator();
474-
{
475-
Set<AbstractDataSet> selected = viewPanel.getDataSetSelector().getSelectedItems();
476-
boolean onlySignatureSelected = !selected.isEmpty();
477-
478-
for (AbstractDataSet ds : selected) {
479-
if (ds instanceof EMSignatureDataSet == false) {
480-
onlySignatureSelected = false;
481-
break;
482-
}
483-
}
484-
485-
JMenuItem mi = new JMenuItem("Remove selected signature gene sets");
486-
mi.addActionListener(evt -> removeSignatureDataSets(map, viewPanel));
487-
mi.setEnabled(onlySignatureSelected);
488-
contextMenu.add(mi);
489-
}
490-
showContextMenu(contextMenu, e);
491-
}
492-
}
493-
});
494-
495-
viewPanel.getChartDataCombo().addItemListener(evt -> {
496-
if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
497-
updating = true;
498-
499-
try {
500-
viewPanel.updateChartCombos();
501-
} finally {
502-
updating = false;
503-
}
504-
505-
updateVisualStyle(map, viewPanel, true);
506-
}
507-
});
508-
viewPanel.getChartTypeCombo().addItemListener(evt -> {
509-
if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
510-
updating = true;
511-
512-
try {
513-
viewPanel.updateChartColorsCombo();
514-
viewPanel.updateChartLabelsCheck();
515-
} finally {
516-
updating = false;
463+
if (updateStyle)
464+
updateVisualStyle(map, viewPanel);
465+
else
466+
netView.updateView();
467+
}
468+
});
469+
470+
viewPanel.getDataSetSelector().getAddButton().addActionListener(evt -> {
471+
postAnalysisPanelMediatorProvider.get().showDialog(viewPanel, netView);
472+
});
473+
viewPanel.getDataSetSelector().getTable().addMouseListener(new MouseAdapter() {
474+
@Override
475+
public void mousePressed(final MouseEvent e) {
476+
maybeShowContextMenu(e);
477+
}
478+
@Override
479+
public void mouseReleased(final MouseEvent e) {
480+
maybeShowContextMenu(e);
481+
}
482+
private void maybeShowContextMenu(final MouseEvent e) {
483+
if (e.isPopupTrigger()) {
484+
final JPopupMenu contextMenu = new JPopupMenu();
485+
{
486+
JMenuItem mi = new JMenuItem("Select nodes and edges from selected data sets");
487+
mi.addActionListener(evt -> selectNodesEdges(viewPanel.getNetworkView(),
488+
viewPanel.getDataSetSelector().getSelectedItems()));
489+
contextMenu.add(mi);
490+
}
491+
contextMenu.addSeparator();
492+
{
493+
Set<AbstractDataSet> selected = viewPanel.getDataSetSelector().getSelectedItems();
494+
boolean onlySignatureSelected = !selected.isEmpty();
495+
496+
for (AbstractDataSet ds : selected) {
497+
if (ds instanceof EMSignatureDataSet == false) {
498+
onlySignatureSelected = false;
499+
break;
517500
}
518-
519-
updateVisualStyle(map, viewPanel, true);
520501
}
521-
});
522-
viewPanel.getChartColorsCombo().addItemListener(evt -> {
523-
if (!updating && evt.getStateChange() == ItemEvent.SELECTED)
524-
updateVisualStyle(map, viewPanel, true);
525-
});
526-
viewPanel.getShowChartLabelsCheck().addActionListener(evt -> {
527-
if (!updating)
528-
updateVisualStyle(map, viewPanel, true);
529-
});
530-
viewPanel.getPublicationReadyCheck().addActionListener(evt -> {
531-
if (!updating)
532-
updateVisualStyle(map, viewPanel);
533-
});
534-
viewPanel.getResetStyleButton().addActionListener(evt -> {
535-
updateVisualStyle(map, viewPanel);
536-
});
537-
viewPanel.getSetEdgeWidthButton().addActionListener(evt -> {
538-
showEdgeWidthDialog();
539-
});
540-
541-
viewPanel.updateChartDataCombo();
502+
503+
JMenuItem mi = new JMenuItem("Remove selected signature gene sets");
504+
mi.addActionListener(evt -> removeSignatureDataSets(map, viewPanel));
505+
mi.setEnabled(onlySignatureSelected);
506+
contextMenu.add(mi);
507+
}
508+
showContextMenu(contextMenu, e);
509+
}
510+
}
511+
});
512+
513+
viewPanel.getChartDataCombo().addItemListener(evt -> {
514+
if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
515+
updating = true;
516+
517+
try {
518+
viewPanel.updateChartCombos();
519+
} finally {
520+
updating = false;
521+
}
522+
523+
updateVisualStyle(map, viewPanel, true);
524+
}
525+
});
526+
viewPanel.getChartTypeCombo().addItemListener(evt -> {
527+
if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
528+
updating = true;
529+
530+
try {
531+
viewPanel.updateChartColorsCombo();
532+
viewPanel.updateChartLabelsCheck();
533+
} finally {
534+
updating = false;
542535
}
536+
537+
updateVisualStyle(map, viewPanel, true);
543538
}
544539
});
540+
viewPanel.getChartColorsCombo().addItemListener(evt -> {
541+
if (!updating && evt.getStateChange() == ItemEvent.SELECTED)
542+
updateVisualStyle(map, viewPanel, true);
543+
});
544+
viewPanel.getShowChartLabelsCheck().addActionListener(evt -> {
545+
if (!updating)
546+
updateVisualStyle(map, viewPanel, true);
547+
});
548+
viewPanel.getPublicationReadyCheck().addActionListener(evt -> {
549+
if (!updating)
550+
updateVisualStyle(map, viewPanel);
551+
});
552+
viewPanel.getResetStyleButton().addActionListener(evt -> {
553+
updateVisualStyle(map, viewPanel);
554+
});
555+
viewPanel.getSetEdgeWidthButton().addActionListener(evt -> {
556+
showEdgeWidthDialog();
557+
});
558+
559+
viewPanel.updateChartDataCombo();
560+
}
561+
562+
/**
563+
* Call this method on the EDT only!
564+
*/
565+
private void setDefaults(EMViewControlPanel viewPanel, EnrichmentMap map) {
566+
List<EMDataSet> dataSets = map.getDataSetList();
567+
568+
if (dataSets.size() > 1) {
569+
ChartData chartData = ChartData.NES_VALUE; // Default for GSEA data sets
570+
EMCreationParameters params = map.getParams();
571+
572+
if (params != null && params.isFDR()) {
573+
Optional<EMDataSet> nonGsea = dataSets.stream()
574+
.filter(ds -> ds.getMethod() != Method.GSEA)
575+
.findFirst();
576+
577+
if (nonGsea.isPresent())
578+
chartData = ChartData.FDR_VALUE; // Default for other data sets
579+
}
580+
581+
viewPanel.getChartDataCombo().setSelectedItem(chartData);
582+
}
545583
}
546584

547585
@AfterInjection

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