protected string GetRatioFile(IQuantificationSummaryOption option, IIdentifiedSpectrum mph)
{
var o18option = option as O18QuantificationSummaryViewerOptions;
string ratioFile = (string)mph.Annotations[o18option.RatioFileKey];
if (ratioFile.Equals("-"))
{
return(null);
}
FileInfo fi = new FileInfo(SummaryFilename);
string result;
if (IsRelativeDir(ratioFile))
{
result = fi.DirectoryName + "/" + ratioFile;
}
else
{
result = fi.DirectoryName + "/" + DefaultDetailDirectory + "/" + ratioFile;
}
result = new FileInfo(result).FullName;
if (!File.Exists(result))
{
return(null);
}
return(result);
}
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);
}
}
protected string GetRatioFile(IQuantificationSummaryOption option, IIdentifiedSpectrum mph)
{
string ratioFile = mph.GetQuantificationItem().Filename;
if (ratioFile.Equals("-"))
{
return(null);
}
FileInfo fi = new FileInfo(SummaryFilename);
string result;
if (IsRelativeDir(ratioFile))
{
result = fi.DirectoryName + "/" + ratioFile;
}
else
{
result = fi.DirectoryName + "/" + DefaultDetailDirectory + "/" + ratioFile;
}
result = new FileInfo(result).FullName;
if (!File.Exists(result))
{
return(null);
}
return(result);
}
public void SetSummaryFilename(string o18SummaryFilename, IAnnotation parentObj)
{
if (this.o18SummaryFilename.Equals(o18SummaryFilename))
{
return;
}
this.parentObj = parentObj;
if (this.summary != null)
{
ClearAllData();
}
this.fileFormat = new O18QuantificationSummaryItemXmlFormat();
this.summary = this.fileFormat.ReadFromFile(o18SummaryFilename);
this.o18SummaryFilename = o18SummaryFilename;
Text = o18SummaryFilename;
this.calc = this.summary.GetCalculator();
this.options = new O18QuantificationSummaryViewerOptions(o18SummaryFilename);
ShowSummary(false);
this.btnSave.Enabled = false;
}
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)
{
IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption;
IIdentifiedResult mr = e.Item as IIdentifiedResult;
panel.InitGraphPane(title, option.Func.ReferenceKey, option.Func.SampleKey, true, 0.0);
try
{
var pplNormal = new PointPairList();
var pplSelected = new PointPairList();
var pplOutlier = new PointPairList();
var groups = (from g in mr
where option.IsProteinRatioValid(g[0])
select g).ToList();
foreach (var group in groups)
{
PointPairList ppl;
if (group.Selected)
{
ppl = pplSelected;
}
else if (option.IsProteinOutlier(group[0]))
{
ppl = pplOutlier;
}
else
{
ppl = pplNormal;
}
double sampleIntensity = option.Func.GetSampleIntensity(group[0]);
double refIntensity = option.Func.GetReferenceIntensity(group[0]);
ppl.Add(refIntensity, sampleIntensity);
ppl[ppl.Count - 1].Tag = group;
Debug.Assert(ppl[ppl.Count - 1].Tag == group);
}
this.panel.ClearData();
this.panel.AddPoints(pplOutlier, OutlierColor, "Outlier");
this.panel.AddPoints(pplSelected, GroupColor, "Current Protein");
this.panel.AddPoints(pplNormal, NormalColor, "Other");
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 lrrr = pplTotal.GetRegression();
PointPairList line = pplTotal.GetRegressionLine(lrrr.Ratio);
var lineItem = this.panel.AddCurve(MyConvert.Format("Ratio={0:0.0000}", lrrr.Ratio), line, Color.Red, SymbolType.None);
}
}
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 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;
IIdentifiedResult mr = e.Item as IIdentifiedResult;
panel.InitGraphPane(title, option.Func.ReferenceKey, option.Func.SampleKey, 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 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 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 = option.Func.GetReferenceIntensity(pep);
double samIntensity = option.Func.GetSampleIntensity(pep);
ppl.Add(refIntensity, samIntensity);
ppl[ppl.Count - 1].Tag = new Pair <IIdentifiedProteinGroup, IIdentifiedSpectrum>(mpg, pep);
maxX = Math.Max(refIntensity, maxX);
}
}
this.panel.ClearData();
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");
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 lrrr = pplTotal.GetRegression();
PointPairList line = pplTotal.GetRegressionLine(lrrr.Ratio);
var lineItem = this.panel.AddCurve(MyConvert.Format("Ratio={0:0.0000}, R2={1:0.0000}", lrrr.Ratio, lrrr.RSquare), line, Color.Red, SymbolType.None);
}
}
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);
}
}
public override void Update(object sender, UpdateQuantificationItemEventArgs e)
{
IQuantificationSummaryOption option = e.Option as IQuantificationSummaryOption;
panel.InitGraphPane(this.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 SilacQuantificationSummaryItemXmlFormat();
foreach (var pep in spectra)
{
if (option.IsPeptideRatioValid(pep))
{
string ratioFile = GetRatioFile(option, pep);
if (ratioFile == null)
{
continue;
}
var item = format.ReadFromFile(ratioFile);
Func <SilacPeakListPair, double> getSamIntensity;
Func <SilacPeakListPair, double> getRefIntensity;
if (item.SampleIsLight)
{
getSamIntensity = m => m.LightIntensity;
getRefIntensity = m => m.HeavyIntensity;
}
else
{
getSamIntensity = m => m.HeavyIntensity;
getRefIntensity = m => m.LightIntensity;
}
PointPairList ppl;
if (pep.Selected)
{
ppl = pplSelected;
}
else
{
ppl = pplNormal;
}
foreach (var envelope in item.ObservedEnvelopes)
{
if (!envelope.Enabled)
{
continue;
}
double refIntensity = getRefIntensity(envelope);
double sampleIntensity = getSamIntensity(envelope);
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 lr = pplTotal.GetRegression();
var lr_text = MyConvert.Format("Ratio={0:0.00}, Correl={1:0.00}, FValue={2:0.00}, FProb={3:E4}", lr.Ratio, lr.RSquare, lr.TValue, lr.PValue);
PointPairList line = pplTotal.GetRegressionLine();
var lineItem = this.panel.AddCurve(lr_text, 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;
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);
}
}
