public override void Update(object sender, UpdateQuantificationItemEventArgs e) { IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption; panel.InitGraphPane(title, option.Func.ReferenceKey, option.Func.SampleKey, true, 0.0); IIdentifiedProteinGroup group = e.Item as IIdentifiedProteinGroup; try { var pplNormal = new PointPairList(); var pplSelected = new PointPairList(); var pplOutlier = new PointPairList(); var spectra = group.GetPeptides(); foreach (var pep in spectra) { if (option.IsPeptideRatioValid(pep)) { PointPairList ppl; if (pep.Selected) { ppl = pplSelected; } else if (option.IsPeptideOutlier(pep)) { ppl = pplOutlier; } else { ppl = pplNormal; } double sampleIntensity = option.Func.GetSampleIntensity(pep); double refIntensity = option.Func.GetReferenceIntensity(pep); ppl.Add(refIntensity, sampleIntensity); ppl[ppl.Count - 1].Tag = pep; Debug.Assert(ppl[ppl.Count - 1].Tag == pep); } } this.panel.ClearData(); this.panel.AddPoints(pplSelected, SelectedColor); this.panel.AddPoints(pplNormal, NormalColor); this.panel.AddPoints(pplOutlier, OutlierColor); var pplTotal = new PointPairList(); pplTotal.AddRange(pplSelected); pplTotal.AddRange(pplNormal); pplTotal.AddRange(pplOutlier); if (pplTotal.Count > 0) { var maxValue = (from p in pplTotal select Math.Max(p.X, p.Y)).Max() * 1.1; this.panel.XAxis.Scale.Max = maxValue; this.panel.YAxis.Scale.Max = maxValue; var ratio = option.GetProteinRatio(group[0]); PointPairList line = pplTotal.GetRegressionLine(ratio); var lineItem = this.panel.AddCurve(option.GetProteinRatioDescription(group[0]), line, RegressionLineColor, SymbolType.None); lineItem.Label.FontSpec = new FontSpec() { Size = 15, Border = new Border() { IsVisible = false } }; } } finally { ZedGraphicExtension.UpdateGraph(this.zgcGraph); } }
public override void Update(object sender, UpdateQuantificationItemEventArgs e) { IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption; panel.InitGraphPane(title, option.Func.ReferenceKey, option.Func.SampleKey, true, 0.0); IIdentifiedProteinGroup group = e.Item as IIdentifiedProteinGroup; try { var pplNormal = new PointPairList(); var pplSelected = new PointPairList(); var spectra = group.GetPeptides(); var format = new O18QuantificationSummaryItemXmlFormat(); foreach (var pep in spectra) { if (pep.IsEnabled(true) && option.IsPeptideRatioValid(pep)) { string ratioFile = GetRatioFile(option, pep); if (ratioFile == null) { continue; } O18QuantificationSummaryItem item = new O18QuantificationSummaryItemXmlFormat().ReadFromFile(ratioFile); item.CalculateIndividualAbundance(); PointPairList ppl; if (pep.Selected) { ppl = pplSelected; } else { ppl = pplNormal; } foreach (var envelope in item.ObservedEnvelopes) { if (!envelope.Enabled) { continue; } double refIntensity = envelope.SampleAbundance.O16; double sampleIntensity = envelope.SampleAbundance.O18; if (refIntensity == 0.0 || sampleIntensity == 0.0) { continue; } ppl.Add(refIntensity, sampleIntensity); ppl[ppl.Count - 1].Tag = pep; Debug.Assert(ppl[ppl.Count - 1].Tag == pep); } } } this.panel.ClearData(); this.panel.AddPoints(pplSelected, SelectedColor); this.panel.AddPoints(pplNormal, NormalColor); var pplTotal = new PointPairList(); pplTotal.AddRange(pplSelected); pplTotal.AddRange(pplNormal); if (pplTotal.Count > 0) { var maxValue = (from p in pplTotal select Math.Max(p.X, p.Y)).Max() * 1.1; this.panel.XAxis.Scale.Max = maxValue; this.panel.YAxis.Scale.Max = maxValue; var ratio = option.GetProteinRatio(group[0]); PointPairList line = pplTotal.GetRegressionLine(ratio); var lineItem = this.panel.AddCurve(option.GetProteinRatioDescription(group[0]), line, RegressionLineColor, SymbolType.None); lineItem.Label.FontSpec = new FontSpec() { Size = 15, Border = new Border() { IsVisible = false } }; } } finally { ZedGraphicExtension.UpdateGraph(this.zgcGraph); } }
public override void Update(object sender, UpdateQuantificationItemEventArgs e) { IIdentifiedResult mr = e.Item as IIdentifiedResult; IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption; string xTitle = MyConvert.Format("(Log({0}) + Log({1})) / 2", option.Func.ReferenceKey, option.Func.SampleKey); string yTitle = MyConvert.Format("Log(Ratio)"); panel.InitGraphPane(title, xTitle, yTitle, true, 0.0); var groups = from g in mr where option.IsProteinRatioValid(g[0]) select g; try { var pplNormal = new PointPairList(); var pplSelected = new PointPairList(); var pplOutlier = new PointPairList(); double maxX = 0.0; foreach (var group in groups) { PointPairList ppl; if (group.Selected) { ppl = pplSelected; } else if (option.IsProteinOutlier(group[0])) { ppl = pplOutlier; } else { ppl = pplNormal; } double int1 = Math.Log(option.Func.GetReferenceIntensity(group[0])); double int2 = Math.Log(option.Func.GetSampleIntensity(group[0])); double A = (int1 + int2) / 2; double ratio = Math.Log(option.GetProteinRatio(group[0])); ppl.Add(A, ratio); ppl[ppl.Count - 1].Tag = group; Debug.Assert(ppl[ppl.Count - 1].Tag == group); maxX = Math.Max(A, maxX); } this.panel.ClearData(); var ratios = (from mpg in groups let ratio = Math.Log(option.GetProteinRatio(mpg[0])) orderby ratio select ratio).ToList(); panel.DrawProbabilityRange(maxX, ratios); this.panel.AddPoints(pplOutlier, OutlierColor, "Outlier"); this.panel.AddPoints(pplSelected, GroupColor, "Current Protein"); this.panel.AddPoints(pplNormal, NormalColor, "Other"); } finally { ZedGraphicExtension.UpdateGraph(this.zgcGraph); } }