public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption;
IIdentifiedResult mr = e.Item as IIdentifiedResult;
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);
try
{
HashSet <IIdentifiedSpectrum> spectra = new HashSet <IIdentifiedSpectrum>();
var groups = from g in mr
where g[0].IsEnabled(true) && option.IsProteinRatioValid(g[0])
select g;
foreach (var mpg in groups)
{
var peptides = from p in mpg.GetPeptides()
where p.IsEnabled(true) && option.IsPeptideRatioValid(p)
select p;
spectra.UnionWith(peptides);
}
List <LSPADItem> items = new List <LSPADItem>();
foreach (var pep in spectra)
{
double refIntensity = Math.Log(option.Func.GetReferenceIntensity(pep));
double sampleIntensity = Math.Log(option.Func.GetSampleIntensity(pep));
double A = (refIntensity + sampleIntensity) / 2;
double ratio = Math.Log(option.GetPeptideRatio(pep));
items.Add(new LSPADItem()
{
LogRatio = ratio,
Intensity = A,
Tag = pep
});
}
LSPADItem.CalculatePValue(items);
//this.panel.DrawProbabilityRange(maxX, ratios);
//this.panel.AddPoints(pplSelected, SelectedColor, "Current Peptide");
//this.panel.AddPoints(pplGroup, GroupColor, "Current Protein");
//this.panel.AddPoints(pplOutlier, OutlierColor, "Outlier");
//this.panel.AddPoints(pplNormal, NormalColor, "Other");
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption;
IIdentifiedResult mr = e.Item as IIdentifiedResult;
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);
try
{
var pplNormal = new PointPairList();
var pplSelected = new PointPairList();
var pplOutlier = new PointPairList();
var pplGroup = new PointPairList();
var groups = from g in mr
where g[0].IsEnabled(true) && option.IsProteinRatioValid(g[0])
select g;
HashSet <IIdentifiedSpectrum> spectra = new HashSet <IIdentifiedSpectrum>();
double maxX = 0.0;
PointPairList ppl;
foreach (var mpg in groups)
{
var peptides = from p in mpg.GetPeptides()
where p.IsEnabled(true) && option.IsPeptideRatioValid(p)
select p;
spectra.UnionWith(peptides);
foreach (var pep in peptides)
{
if (pep.Selected)
{
ppl = pplSelected;
}
else if (mpg.Selected)
{
ppl = pplGroup;
}
else if (option.IsPeptideOutlier(pep))
{
ppl = pplOutlier;
}
else
{
ppl = pplNormal;
}
double refIntensity = Math.Log(option.Func.GetReferenceIntensity(pep));
double sampleIntensity = Math.Log(option.Func.GetSampleIntensity(pep));
double A = (refIntensity + sampleIntensity) / 2;
double ratio = Math.Log(option.GetPeptideRatio(pep));
ppl.Add(A, ratio);
ppl[ppl.Count - 1].Tag = new Pair <IIdentifiedProteinGroup, IIdentifiedSpectrum>(mpg, pep);
maxX = Math.Max(A, maxX);
}
}
this.panel.ClearData();
var ratios = (from pep in spectra
let ratio = Math.Log(option.GetPeptideRatio(pep))
orderby ratio
select ratio).ToList();
this.panel.DrawProbabilityRange(maxX, ratios);
this.panel.AddPoints(pplSelected, SelectedColor, "Current Peptide");
this.panel.AddPoints(pplGroup, GroupColor, "Current Protein");
this.panel.AddPoints(pplOutlier, OutlierColor, "Outlier");
this.panel.AddPoints(pplNormal, NormalColor, "Other");
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
