Fixes to the Relative Abundance graph formatting

pwiz_tools/Skyline/Controls/Graphs/SummaryRelativeAbundanceGraphPane.cs

@@ -219,19 +219,25 @@ public override void UpdateGraph(bool selectionChanged)
 
             var document = GraphSummary.DocumentUIContainer.DocumentUI;
             var graphSettings = GraphSettings.FromSettings();
+            var aggregateOp = GraphValues.AggregateOp.FromCurrentSettings();
 
             // Only create graph data (and recalculate abundances)
             // if settings have changed, the document has changed, or if it
             // is not yet created
+            var dataChanged = false;
+            var oldGraphData = _graphData;
             if (_graphData?.GraphPointList == null ||
                 !ReferenceEquals(document, _graphData.Document) ||
-                !Equals(graphSettings, _graphData.GraphSettings))
+                !Equals(graphSettings, _graphData.GraphSettings) ||
+                !Equals(_graphData.AggregateOp, aggregateOp))
             {
                 _graphData = CreateGraphData(document, graphSettings);
             }
+
             // Calculate y values and order which can change based on the
             // replicate display option or the show CV option
             _graphData.CalcDataPositions(GraphSummary.ResultsIndex, selectedProtein);
+            dataChanged = _graphData.MinY != oldGraphData?.MinY || _graphData.MaxY != oldGraphData?.MaxY;
 
             // For proper z-order, add the selected points, then the matched points, then the unmatched points
             var selectedPoints = new PointPairList();
@@ -278,7 +284,8 @@ public override void UpdateGraph(bool selectionChanged)
                 }
             }
             AddPoints(new PointPairList(unmatchedPoints), Color.Gray, DotPlotUtil.PointSizeToFloat(PointSize.normal), false, PointSymbol.Circle);
-            UpdateAxes();
+            if(dataChanged || Settings.Default.RelativeAbundanceLogScale != YAxis.Scale.IsLog)
+                UpdateAxes();
             if (Settings.Default.GroupComparisonAvoidLabelOverlap)
                 AdjustLabelSpacings(_labeledPoints, GraphSummary.GraphControl);
             else
@@ -357,7 +364,14 @@ protected virtual void UpdateAxes()
             YAxis.Scale.MinAuto = true;
             XAxis.Scale.MaxAuto = true;
             XAxis.Scale.MinAuto = true;
-            if (Settings.Default.AreaLogScale )
+
+            if (CurveList.FirstOrDefault() is LineItem curve)
+            {
+                // if markers are overlapping leave a little space between the X axis and the first marker
+                if(curve.Symbol.Size * _graphData.PointPairList.Count > Chart.Rect.Width)
+                    XAxis.Scale.Min = -(_graphData.PointPairList.Last().X - _graphData.PointPairList.First().X) * 0.02;
+            }
+            if (Settings.Default.RelativeAbundanceLogScale )
             {
                 YAxis.Title.Text = TextUtil.SpaceSeparate(GraphsResources.SummaryPeptideGraphPane_UpdateAxes_Log, YAxis.Title.Text);
                 YAxis.Type = AxisType.Log;
@@ -436,6 +450,7 @@ protected GraphData(SrmDocument document, GraphSettings graphSettings)
             {
                 Document = document;
                 GraphSettings = graphSettings;
+                AggregateOp = GraphValues.AggregateOp.FromCurrentSettings();
                 var schema = SkylineDataSchema.MemoryDataSchema(document, SkylineDataSchema.GetLocalizedSchemaLocalizer());
                 bool anyMolecules = document.HasSmallMolecules;
                 // Build the list of points to show.
@@ -475,6 +490,7 @@ protected GraphData(SrmDocument document, GraphSettings graphSettings)
 
             public SrmDocument Document { get; }
             public GraphSettings GraphSettings { get; }
+            public GraphValues.AggregateOp AggregateOp { get; }
 
             public void CalcDataPositions(int iResult, PeptideGroupDocNode selectedProtein)
             {

pwiz_tools/Skyline/Properties/Settings.settings

@@ -884,5 +884,8 @@
     <Setting Name="GroupComparisonSuspendLabelLayout" Type="System.Boolean" Scope="User">
       <Value Profile="(Default)">False</Value>
     </Setting>
+    <Setting Name="RelativeAbundanceLogScale" Type="System.Boolean" Scope="User">
+      <Value Profile="(Default)">True</Value>
+    </Setting>	
   </Settings>
 </SettingsFile>

pwiz_tools/Skyline/Skyline.resx

@@ -923,6 +923,12 @@
   <data name="peptideLogScaleContextMenuItem.Text" xml:space="preserve">
     <value>Log Scale</value>
   </data>
+  <data name="relativeAbundanceLogScaleContextMenuItem.Size" type="System.Drawing.Size, System.Drawing">
+    <value>209, 22</value>
+  </data>
+  <data name="relativeAbundanceLogScaleContextMenuItem.Text" xml:space="preserve">
+    <value>Log Scale</value>
+  </data>
   <data name="peptideCvsContextMenuItem.Size" type="System.Drawing.Size, System.Drawing">
     <value>209, 22</value>
   </data>
@@ -2967,6 +2973,12 @@
   <data name="&gt;&gt;showDotProductToolStripMenuItem.Type" xml:space="preserve">
     <value>System.Windows.Forms.ToolStripMenuItem, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089</value>
   </data>
+  <data name="&gt;&gt;relativeAbundanceLogScaleContextMenuItem.Name" xml:space="preserve">
+    <value>relativeAbundanceLogScaleContextMenuItem</value>
+  </data>
+  <data name="&gt;&gt;relativeAbundanceLogScaleContextMenuItem.Type" xml:space="preserve">
+    <value>System.Windows.Forms.ToolStripMenuItem, System.Windows.Forms, Version=4.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089</value>
+  </data>
   <data name="&gt;&gt;peptideLogScaleContextMenuItem.Name" xml:space="preserve">
     <value>peptideLogScaleContextMenuItem</value>
   </data>

pwiz_tools/Skyline/SkylineGraphs.cs

@@ -3918,8 +3918,16 @@ private void BuildAreaGraphMenu(GraphSummary graphSummary, ToolStrip menuStrip,
                     peptideCvsContextMenuItem.Checked = set.ShowPeptideCV;
                 }
 
-                menuStrip.Items.Insert(iInsert++, peptideLogScaleContextMenuItem);
-                peptideLogScaleContextMenuItem.Checked = set.AreaLogScale;
+                if (graphType != GraphTypeSummary.abundance)
+                {
+                    menuStrip.Items.Insert(iInsert++, peptideLogScaleContextMenuItem);
+                    peptideLogScaleContextMenuItem.Checked = set.AreaLogScale;
+                }
+                else
+                {
+                    menuStrip.Items.Insert(iInsert++, relativeAbundanceLogScaleContextMenuItem);
+                    relativeAbundanceLogScaleContextMenuItem.Checked = set.RelativeAbundanceLogScale;
+                }
                 selectionContextMenuItem.Checked = set.ShowReplicateSelection;
                 menuStrip.Items.Insert(iInsert++, selectionContextMenuItem);
                 if (graphType == GraphTypeSummary.abundance)
@@ -4636,6 +4644,17 @@ public void ShowPeptideLogScale(bool isChecked)
             UpdateSummaryGraphs();
         }
 
+        private void relativeAbundanceLogScaleContextMenuItem_Click(object sender, EventArgs e)
+        {
+            ShowRelativeAbundanceLogScale(relativeAbundanceLogScaleContextMenuItem.Checked);
+        }
+
+        public void ShowRelativeAbundanceLogScale(bool isChecked)
+        {
+            Settings.Default.RelativeAbundanceLogScale = isChecked ;
+            UpdateRelativeAbundanceGraphs();
+        }
+
         private void peptideCvsContextMenuItem_Click(object sender, EventArgs e)
         {
             ShowCVValues(peptideCvsContextMenuItem.Checked);
@@ -4764,6 +4783,10 @@ public void UpdatePeakAreaGraph()
             _listGraphPeakArea.ForEach(g => g.UpdateUI());
         }
 
+        public void UpdateRelativeAbundanceGraphs()
+        {
+            _listGraphPeakArea.FindAll(g => g.Type == GraphTypeSummary.abundance).ForEach(g => g.UpdateUI());
+        }
         private void UpdateSummaryGraphs()
         {
             UpdateRetentionTimeGraph();

pwiz_tools/Skyline/app.config

@@ -873,6 +873,9 @@
             <setting name="GroupComparisonAvoidLabelOverlap" serializeAs="String">
                 <value>True</value>
             </setting>
+            <setting name="RelativeAbundanceLogScale" serializeAs="String">
+                 <value>True</value>
+            </setting>			
         </pwiz.Skyline.Properties.Settings>
     </userSettings>
     <applicationSettings>