Two New MetaDraw Plots: Histogram of Ambiguity Levels and Histogram of Notch (#2679)

* gitignore

* Add Collision Energy column to PSM TSV output

Parse collisional energy from MsDataScan.HcdEnergy into a new nullable CollisionalEnergy property on SpectralMatch. Write the column conditionally (only when at least one scan has data) using the same pattern as 1/K0.

* Add unit tests for collisional energy TSV column

Six tests covering parsed from scan, null when absent, null when invalid, column present with flag, column absent by default, N/A when missing.

* Add Collision Energy as a grouping property in MetaDraw data visualization

* ambiguity

* Notch Plot

* more tests

Author: nbollis

MetaMorpheus/GuiFunctions/MetaDraw/PlotModelStat.cs

@@ -43,7 +43,9 @@ public class PlotModelStat
             "Histogram of Missed Cleavages",
             "Histogram of Fragment Ion Types by Count",
             "Histogram of Fragment Ion Types by Intensity",
-            "Histogram of Ids by Retention Time"
+            "Histogram of Ids by Retention Time",
+            "Histogram of Spectral Match Ambiguity Levels",
+            "Histogram of Notch (Ambiguous PSMs Split Across Notches)"
         };
 
         public PlotModel Model => privateModel;
@@ -124,6 +126,12 @@ private void createPlot(string plotType)
                 case "Histogram of Ids by Retention Time":
                     histogramPlot(12);
                     break;
+                case "Histogram of Spectral Match Ambiguity Levels":
+                    histogramPlot(13);
+                    break;
+                case "Histogram of Notch (Ambiguous PSMs Split Across Notches)":
+                    histogramPlot(14);
+                    break;
             }
         }
 
@@ -153,7 +161,7 @@ private void histogramPlot(int plotType)
             int[] totalCounts;
             int categoriesPerGroup = 0;
             List<string> allGroupKeys = null;
-            bool isCategoryHistogram = plotType == 5 || plotType == 10 || plotType == 11;
+            bool isCategoryHistogram = plotType == 5 || plotType == 10 || plotType == 11 || plotType == 13;
 
             if (isCategoryHistogram)
             {
@@ -336,6 +344,34 @@ private HistogramRawData GetHistogramData(int plotType)
                         dictsBySourceFile.Add(fileName, result);
                     }
                     break;
+                case 13: // Histogram of Spectral Match Ambiguity Levels
+                    xAxisTitle = "Ambiguity Level";
+                    labelAngle = 0;
+                    foreach (var fileName in psmsBySourceFile.Keys)
+                    {
+                        var result = psmsBySourceFile[fileName]
+                            .GroupBy(p => NormalizeAmbiguityLevel(p.AmbiguityLevel))
+                            .ToDictionary(p => p.Key, p => p.Count());
+                        dictsBySourceFile.Add(fileName, result);
+                    }
+                    break;
+                case 14: // Histogram of Notch (ambiguous PSMs contribute to each of their pipe-delimited notches)
+                    xAxisTitle = "Notch";
+                    binSize = 1;
+                    labelAngle = 0;
+                    foreach (var fileName in psmsBySourceFile.Keys)
+                    {
+                        var values = new List<double>();
+                        foreach (var psm in psmsBySourceFile[fileName])
+                        {
+                            foreach (double notch in ParseAmbiguousNotchValues(psm.Notch))
+                                values.Add(notch);
+                        }
+                        numbersBySourceFile.Add(fileName, values);
+                        var results = values.GroupBy(p => roundToBin(p, binSize)).OrderBy(p => p.Key).Select(p => p);
+                        dictsBySourceFile.Add(fileName, results.ToDictionary(p => p.Key.ToString(CultureInfo.InvariantCulture), v => v.Count()));
+                    }
+                    break;
             }
 
             return new HistogramRawData(xAxisTitle, yAxisTitle, binSize, labelAngle, numbersBySourceFile, dictsBySourceFile);
@@ -515,6 +551,13 @@ private Dictionary<string, int> GetCategoryDictForGroup(int plotType, Observable
                 return mods.GroupBy(p => p.IdWithMotif).ToDictionary(p => p.Key, v => v.Count());
             }
 
+            if (plotType == 13)
+            {
+                return groupPsms
+                    .GroupBy(p => NormalizeAmbiguityLevel(p.AmbiguityLevel))
+                    .ToDictionary(p => p.Key, p => p.Count());
+            }
+
             var allMatchedIons = groupPsms.SelectMany(p => p.MatchedIons).ToList();
             if (plotType == 10)
             {
@@ -1013,6 +1056,7 @@ private IEnumerable<double> GetNumbersFromPsms(ObservableCollection<SpectrumMatc
                 8 => GetHydrophobicityScores(psms),
                 9 => psms.Where(p => !p.MissedCleavage.Contains("|")).Select(p => double.Parse(p.MissedCleavage)),
                 12 => psms.Select(p => (double)(int)Math.Round(p.RetentionTime, 0)),
+                14 => psms.SelectMany(p => ParseAmbiguousNotchValues(p.Notch)),
                 _ => Enumerable.Empty<double>()
             };
         }
@@ -1042,6 +1086,37 @@ public HistItem(double value, int categoryIndex, string bin, int total, string g
             }
         }
 
+        private static IEnumerable<string> SplitAmbiguousNotch(string notch)
+        {
+            if (string.IsNullOrWhiteSpace(notch))
+                return new[] { "0" };
+
+            return notch.Split('|')
+                .Select(p => p.Trim())
+                .Where(p => p.Length > 0)
+                .DefaultIfEmpty("0");
+        }
+
+        private static IEnumerable<double> ParseAmbiguousNotchValues(string notch)
+        {
+            foreach (var part in SplitAmbiguousNotch(notch))
+            {
+                if (double.TryParse(part, NumberStyles.Float, CultureInfo.InvariantCulture, out double value))
+                    yield return value;
+                else
+                    yield return 0.0;
+            }
+        }
+
+        private static string NormalizeAmbiguityLevel(string ambiguityLevel)
+        {
+            if (string.IsNullOrWhiteSpace(ambiguityLevel))
+                return "1";
+
+            var first = ambiguityLevel.Split('|')[0].Trim();
+            return string.IsNullOrEmpty(first) ? "1" : first;
+        }
+
         /// <summary>
         /// Orders strings numerically if all values are numeric, otherwise alphabetically.
         /// </summary>