Show protein context above precursor list in QC plots

src/org/labkey/targetedms/TargetedMSController.java

@@ -874,6 +874,7 @@ public static class LeveyJenningsPlotOptions
         private Integer _trailingRuns;
         private Integer _calendarMonthsToShow;
         private String _heatmapDataSource;
+        private String _hiddenSeries;
 
         public Map<String, String> getAsMapOfStrings()
         {
@@ -906,6 +907,8 @@ public Map<String, String> getAsMapOfStrings()
                 valueMap.put("calendarMonthsToShow", Integer.toString(_calendarMonthsToShow));
             if (_heatmapDataSource != null)
                 valueMap.put("heatMapDataSource", _heatmapDataSource);
+            if (_hiddenSeries != null)
+                valueMap.put("hiddenSeries", _hiddenSeries);
             // note: start and end date handled separately since they can be null and we want to persist that
             return valueMap;
         }
@@ -1034,6 +1037,16 @@ public void setHeatmapDataSource(String heatmapDataSource)
         {
             _heatmapDataSource = heatmapDataSource;
         }
+
+        public String getHiddenSeries()
+        {
+            return _hiddenSeries;
+        }
+
+        public void setHiddenSeries(String hiddenSeries)
+        {
+            _hiddenSeries = hiddenSeries;
+        }
     }
 
     @RequiresPermission(ReadPermission.class)

src/org/labkey/targetedms/model/QCPlotFragment.java

@@ -21,6 +21,12 @@ public class QCPlotFragment
     private List<GuideSetStats> guideSetStats;
     @Nullable
     private Color _seriesColor;
+    @Nullable
+    private Long precursorRowId;
+    @Nullable
+    private Long peptideGroupId;
+    @Nullable
+    private String peptideGroupLabel;
 
     public String getSeriesLabel()
     {
@@ -77,6 +83,11 @@ public JSONObject toJSON(boolean includeLJ, boolean includeMR, boolean includeMe
         JSONObject jsonObject = new JSONObject();
         jsonObject.put("DataType", getDataType());
         jsonObject.put("SeriesLabel", getSeriesLabel());
+        if (peptideGroupId != null)
+        {
+            jsonObject.put("PeptideGroupId", peptideGroupId);
+            jsonObject.put("PeptideGroupLabel", peptideGroupLabel != null ? peptideGroupLabel : "");
+        }
         if (_seriesColor != null)
         {
             jsonObject.put("SeriesColor", "#" + Integer.toHexString(_seriesColor.getRGB()).substring(2).toUpperCase());
@@ -205,4 +216,37 @@ public Color getSeriesColor()
     {
         return _seriesColor;
     }
+
+    @Nullable
+    public Long getPrecursorRowId()
+    {
+        return precursorRowId;
+    }
+
+    public void setPrecursorRowId(Long precursorRowId)
+    {
+        this.precursorRowId = precursorRowId;
+    }
+
+    @Nullable
+    public Long getPeptideGroupId()
+    {
+        return peptideGroupId;
+    }
+
+    public void setPeptideGroupId(Long peptideGroupId)
+    {
+        this.peptideGroupId = peptideGroupId;
+    }
+
+    @Nullable
+    public String getPeptideGroupLabel()
+    {
+        return peptideGroupLabel;
+    }
+
+    public void setPeptideGroupLabel(String peptideGroupLabel)
+    {
+        this.peptideGroupLabel = peptideGroupLabel;
+    }
 }

src/org/labkey/targetedms/outliers/OutlierGenerator.java

@@ -44,9 +44,11 @@
 import org.labkey.targetedms.model.SampleFileQCMetadata;
 import org.labkey.targetedms.parser.GeneralMolecule;
 import org.labkey.targetedms.parser.GeneralPrecursor;
+import org.labkey.targetedms.parser.PeptideGroup;
 import org.labkey.targetedms.parser.SampleFile;
 import org.labkey.targetedms.query.MoleculeManager;
 import org.labkey.targetedms.query.MoleculePrecursorManager;
+import org.labkey.targetedms.query.PeptideGroupManager;
 import org.labkey.targetedms.query.PeptideManager;
 import org.labkey.targetedms.query.PrecursorManager;
 
@@ -539,7 +541,11 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
             Optional<RawMetricDataSet> bestPrecursorIdRow = entry.getValue().stream().filter(x -> x.getPrecursorId() != null).min(Comparator.comparing(RawMetricDataSet::getPrecursorId));
 
             // Remember the precursor ID so that we can assign a series color based on Skyline's algorithm
-            bestPrecursorIdRow.ifPresent(rawMetricDataSet -> fragmentsByPrecursorId.put(rawMetricDataSet.getPrecursorId(), qcPlotFragment));
+            // and to sort by Skyline document order (row ID) instead of alphabetically
+            bestPrecursorIdRow.ifPresent(rawMetricDataSet -> {
+                fragmentsByPrecursorId.put(rawMetricDataSet.getPrecursorId(), qcPlotFragment);
+                qcPlotFragment.setPrecursorRowId(rawMetricDataSet.getPrecursorId());
+            });
 
             qcPlotFragment.setSeriesLabel(entry.getKey());
             qcPlotFragment.setQcPlotData(entry.getValue());
@@ -588,10 +594,21 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
                 Color color = ColorGenerator.getColor(molecule.getTextId(), seriesColors);
                 entry.getValue().setSeriesColor(color);
                 seriesColors.add(color);
+
+                // set the peptide group (protein / molecule list) for the combined plot tree legend
+                PeptideGroup peptideGroup = PeptideGroupManager.getPeptideGroup(c, molecule.getPeptideGroupId());
+                if (peptideGroup != null)
+                {
+                    entry.getValue().setPeptideGroupId(peptideGroup.getId());
+                    entry.getValue().setPeptideGroupLabel(peptideGroup.getLabel());
+                }
             }
         }
 
-        qcPlotFragments.sort(Comparator.comparing(QCPlotFragment::getSeriesLabel));
+        // Sort by precursor row ID to preserve Skyline document order. Fragments with no precursor ID
+        // (e.g. trace metrics) fall back to alphabetical order after all precursor-scoped series.
+        qcPlotFragments.sort(Comparator.comparing(QCPlotFragment::getPrecursorRowId, Comparator.nullsLast(Comparator.naturalOrder()))
+                .thenComparing(QCPlotFragment::getSeriesLabel));
         return qcPlotFragments;
     }
 

webapp/TargetedMS/css/qcTrendPlotReport.css

@@ -102,4 +102,17 @@
 
 .x4-panel-header-text-container-default {
   font-weight: normal;
+}
+
+.qc-combined-tree-legend {
+    background: white;
+    line-height: 1.4;
+}
+
+.qc-combined-tree-legend .qc-tree-group label:hover {
+    background-color: #f0f0f0;
+}
+
+.qc-combined-tree-legend .qc-tree-precursor:hover {
+    background-color: #f0f0f0;
 }

webapp/TargetedMS/js/QCPlotHelperBase.js

@@ -412,9 +412,11 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
         }
 
         if (this.singlePlot && this.getMetricPropsById(this.metric).precursorScoped) {
+            this.peptideGroups = this.buildPeptideGroups();
             addedPlot = this.addCombinedPeptideSinglePlot(metricProps);
         }
         else {
+            this.peptideGroups = null;
             addedPlot = this.addIndividualPrecursorPlots(metricProps);
         }
 
@@ -822,6 +824,8 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
         const plot = LABKEY.vis.TrendingLinePlot(plotConfig);
         plot.render();
 
+        this.attachCombinedLegendClickHandlers();
+
         this.addAnnotationsToPlot(plot, combinePlotData);
 
         this.addGuideSetTrainingRangeToPlot(plot, combinePlotData);

webapp/TargetedMS/js/QCPlotHelperWrapper.js

@@ -215,6 +215,11 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperWrapper", {
         }
 
         this.setPlotBrushingDisplayStyle();
+
+        if (this.hasPeptideGroupTree()) {
+            this.renderCombinedTreeLegend(id, legendMargin);
+        }
+
         return true;
     },
 
@@ -295,6 +300,12 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperWrapper", {
             this.fragmentPlotData[fragment] = this.getInitFragmentPlotData(fragment, dataType, mz, color);
         }
 
+        // Store peptide group info (protein / molecule list) for the combined plot tree legend
+        if (this.fragmentPlotData[fragment].peptideGroupId == null && plotDataRow['PeptideGroupId'] != null) {
+            this.fragmentPlotData[fragment].peptideGroupId = plotDataRow['PeptideGroupId'];
+            this.fragmentPlotData[fragment].peptideGroupLabel = plotDataRow['PeptideGroupLabel'];
+        }
+
         var metricId = row['MetricId'];
         const metricProp = metricProps[metricId];