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());
@@ -559,6 +565,7 @@ public List<QCPlotFragment> getQCPlotFragment(List<RawMetricDataSet> rawMetricDa
         // Now that we have all the precursor IDs, in order (important so that we de-dupe the colors in a stable order),
         // run through them and choose a color
         Set<Color> seriesColors = new HashSet<>();
+        Map<Long, PeptideGroup> peptideGroupCache = new HashMap<>();
         for (Map.Entry<Long, QCPlotFragment> entry : fragmentsByPrecursorId.entrySet())
         {
             long precursorId = entry.getKey();
@@ -588,10 +595,21 @@ 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 = peptideGroupCache.computeIfAbsent(molecule.getPeptideGroupId(), id -> PeptideGroupManager.getPeptideGroup(c, id));
+                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;
     }
 

test/src/org/labkey/test/tests/targetedms/TargetedMSExperimentalQCLinkTest.java

@@ -100,8 +100,8 @@ public void testLinkExperimentalQC()
         String expRange = "Skyline File: " + SProCoP_FILE + ", " +
                 "Start: 2013-08-09 11:39:00, " +
                 "End: 2013-08-27 14:45:49, " +
-                "Mean: 14.669, Std Dev: 0.501, " +
-                "%CV: 3.415";
+                "Mean: 28.764, Std Dev: 0.666, " +
+                "%CV: 2.315";
 
         goToProjectHome(QC_FOLDER_1);
         PanoramaDashboard qcDashboard = new PanoramaDashboard(this);
@@ -114,16 +114,16 @@ public void testLinkExperimentalQC()
                         "Start: 2013-08-03 00:00:00, " +
                         "End: 2013-08-09 23:59:00, " +
                         "# Runs: 5, " +
-                        "Mean: 15.427, " +
-                        "Std Dev: 0.973, " +
-                        "%CV: 6.307",
+                        "Mean: 32.798, " +
+                        "Std Dev: 7.613, " +
+                        "%CV: 23.212",
                 "Guide Set ID: " + getGuideSetRowId("Second") + ", " +
                         "Start: 2013-08-19 00:00:00, " +
                         "End: 2013-08-21 23:59:00, " +
                         "# Runs: 17, " +
-                        "Mean: 14.687, " +
-                        "Std Dev: 0.588, " +
-                        "%CV: 4.004");
+                        "Mean: 28.854, " +
+                        "Std Dev: 0.675, " +
+                        "%CV: 2.339");
 
         goToProjectHome();
         DataRegionTable table = new DataRegionTable("TargetedMSRuns", getDriver());

test/src/org/labkey/test/tests/targetedms/TargetedMSTrailingMeanAndCVTest.java

@@ -93,9 +93,9 @@ public void testTrailingMeanPlotType()
                 Metric:
                 Retention Time
                 Peptide:
-                ATEEQLK ++, 409.7163
+                VYVEELKPTPEGDLEILLQK ++, 1,157.1330
                 Value:
-                15.652
+                35.156
                 Replicate:
                 3 runs average
                 Acquired:
@@ -117,9 +117,9 @@ public void testTrailingMeanPlotType()
                 Metric:
                 Retention Time
                 Peptide:
-                ATEEQLK ++, 409.7163
+                VYVEELKPTPEGDLEILLQK ++, 1,157.1330
                 Value:
-                15.684
+                35.102
                 Replicate:
                 3 runs average
                 Acquired:
@@ -160,9 +160,9 @@ public void testTrailingCVPlotType()
                 Metric:
                 Retention Time
                 Peptide:
-                ATEEQLK ++, 409.7163
+                VYVEELKPTPEGDLEILLQK ++, 1,157.1330
                 Value:
-                6.831
+                22.645
                 Replicate:
                 3 runs average
                 Acquired:
@@ -183,9 +183,9 @@ public void testTrailingCVPlotType()
                 Metric:
                 Retention Time
                 Peptide:
-                ATEEQLK ++, 409.7163
+                VYVEELKPTPEGDLEILLQK ++, 1,157.1330
                 Value:
-                3.704
+                2.225
                 Replicate:
                 3 runs average
                 Acquired:

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

@@ -8,7 +8,12 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
     statics: {
         qcPlotTypes : ['Metric Value', 'Moving Range', 'CUSUMm', 'CUSUMv', 'Trailing CV', 'Trailing Mean'],
         maxPointsPerSeries : 300,
-        shapeDomain: ['Include', 'Exclude', 'Include-Outlier', 'Exclude-Outlier']
+        shapeDomain: ['Include', 'Exclude', 'Include-Outlier', 'Exclude-Outlier'],
+        // Separates fragment from series name in legend item names (e.g. "PEPTIDE|Left"). Fragments are peptide
+        // sequences or molecule names and are not expected to contain this character.
+        SERIES_NAME_SEP: '|',
+        // Square 12x12 shape for combined plot legend swatches, matching the tree legend checkbox size.
+        SQUARE_LEGEND_SHAPE: function() { return 'M-6,-6 L6,-6 6,6 -6,6 Z'; }
     },
 
     showMetricValuePlot: function() {
@@ -412,9 +417,11 @@ 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);
         }
 
@@ -602,10 +609,11 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
                 const series1Legend = precursorInfo.dataType === 'Peptide' ? proteomicsLegend : ionLegend;
 
                 series1Legend.push({
-                    name: precursorInfo.fragment + (this.isMultiSeries() ? '|' + legendSeries[0] : ''),
+                    name: precursorInfo.fragment + (this.isMultiSeries() ? LABKEY.targetedms.QCPlotHelperBase.SERIES_NAME_SEP + legendSeries[0] : ''),
                     text: this.legendHelper.getLegendItemText(precursorInfo),
                     hoverText: precursorInfo.fragment,
-                    color: groupColors[i % groupColors.length]
+                    color: groupColors[i % groupColors.length],
+                    shape: LABKEY.targetedms.QCPlotHelperBase.SQUARE_LEGEND_SHAPE
                 });
             }
         }
@@ -628,10 +636,11 @@ Ext4.define("LABKEY.targetedms.QCPlotHelperBase", {
 
                 precursorInfo = this.fragmentPlotData[this.precursors[i]];
                 series2Legend.push({
-                    name: precursorInfo.fragment + '|' + legendSeries[1],
+                    name: precursorInfo.fragment + LABKEY.targetedms.QCPlotHelperBase.SERIES_NAME_SEP + legendSeries[1],
                     text: this.legendHelper.getLegendItemText(precursorInfo),
                     hoverText: precursorInfo.fragment,
-                    color: groupColors[(this.precursors.length + i) % groupColors.length]
+                    color: groupColors[(this.precursors.length + i) % groupColors.length],
+                    shape: LABKEY.targetedms.QCPlotHelperBase.SQUARE_LEGEND_SHAPE
                 });
             }
         }
@@ -822,6 +831,8 @@ 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];