public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
panel.ClearData();
var summary = e.Item as IsobaricItem;
if (null != summary)
{
if (summary.PeakInIsolationWindow.Count > 0)
{
var pplWinPrecursor = new PointPairList();
foreach (var peak in summary.PeakInIsolationWindow)
{
if (peak.Tag > 0)
{
pplWinPrecursor.Add(new PointPair(peak.Mz, peak.Intensity, string.Format("{0:0.00000}", peak.Mz)));
}
else
{
pplWinPrecursor.Add(new PointPair(peak.Mz, peak.Intensity));
}
}
panel.AddIndividualLine("", pplWinPrecursor, Color.Black, Color.Blue);
panel.Title.Text = string.Format("Isolation Window (Specifity = {0:0.00}%)", summary.PrecursorPercentage * 100);
}
}
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
protected void OnUpdateSpectrum(UpdateQuantificationItemEventArgs e)
{
if (UpdateSpectrum != null)
{
UpdateSpectrum(this, e);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.ClearData();
try
{
int firstScan = summary.ObservedEnvelopes.First().Scan;
int lastScan = summary.ObservedEnvelopes.Last().Scan;
var ppms = summary.GetPPMList();
var O16PPMs = GetPoints(firstScan, lastScan, ppms, m => m.O16);
var O181PPMs = GetPoints(firstScan, lastScan, ppms, m => m.O181);
var O182PPMs = GetPoints(firstScan, lastScan, ppms, m => m.O182);
panel.AddCurve("O16", O16PPMs, O18QuantificationConstants.COLOR_O16, SymbolType.None);
panel.AddCurve("O18(1)", O181PPMs, O18QuantificationConstants.COLOR_O18_1, SymbolType.None);
panel.AddCurve("O18(2)", O182PPMs, O18QuantificationConstants.COLOR_O18_2, SymbolType.None);
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
private void DoUpdateItem()
{
foreach (ListViewItem item in lvExperimentalScans.Items)
{
(item.Tag as QuanEnvelope).IsSelected = item.Selected;
}
var e = new UpdateQuantificationItemEventArgs(options, summary);
OnUpdateItem(e);
}
private void DoUpdateProtein(TreeNode node, bool forceRefresh = false)
{
if (proteinNode != node || forceRefresh)
{
proteinNode = node;
var args = new UpdateQuantificationItemEventArgs(option, node.Tag);
new ZedGraphITraqProtein2(zgcProtein, this.CreateGraphics(), "Protein").Update(null, args);
}
}
private void DoUpdateUniquePeptide(TreeNode node, bool forceRefresh = false)
{
if (uniquePeptideNode != node || forceRefresh)
{
var args = new UpdateQuantificationItemEventArgs(option, node.Tag);
new ZedGraphITraqProtein2(zgcUniquePeptide, this.CreateGraphics(), "Unique Peptide").Update(null, args);
uniquePeptideNode = node;
DoUpdateProtein(node.Parent);
}
}
private void DoUpdateSpectrum(TreeNode node)
{
var spectrum = node.Tag as IIdentifiedSpectrum;
var itraqItem = spectrum.FindIsobaricItem();
var args = new UpdateQuantificationItemEventArgs(null, itraqItem);
OnUpdateSpectrum(args);
DoUpdateUniquePeptide(node.Parent);
DoUpdateProtein(node.Parent.Parent);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
var pplRed = new PointPairList();
var pplGreen = new PointPairList();
var enabled = summary.ObservedEnvelopes.FindAll(m => m.Enabled);
enabled.ForEach(m =>
{
PointPairList ppl = m.IsSelected ? pplGreen : pplRed;
if (summary.SampleIsLight)
{
ppl.Add(new PointPair(m.HeavyIntensity, m.LightIntensity, 0.0, m));
}
else
{
ppl.Add(new PointPair(m.LightIntensity, m.HeavyIntensity, 0.0, m));
}
});
ZedGraphicExtension.ClearData(this.zgcGraph, false);
AddCurve(pplGreen, SilacQuantificationConstants.REFERENCE_COLOR);
AddCurve(pplRed, SilacQuantificationConstants.SAMPLE_COLOR);
var pplTotal = new PointPairList();
pplTotal.AddRange(pplRed);
pplTotal.AddRange(pplGreen);
if (pplTotal.Count > 0)
{
PointPairList line = ZedGraphicExtension.GetRegressionLine(pplTotal, summary.Ratio);
ZedGraphicExtension.AddDataToLine(this.zgcGraph, MyConvert.Format("Ratio = {0:0.0000}, Correlation = {1:0.0000}", summary.Ratio,
summary.RegressionCorrelation), line, SilacQuantificationConstants.IDENTIFIED_COLOR, false);
}
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var spectra = e.Item as IEnumerable <IIdentifiedSpectrum>;
if (spectra == null)
{
throw new ArgumentException("e.Item should be IEnumerable<IIdentifiedSpectrum>");
}
var validItems = (from spectrum in spectra
let item = spectrum.FindIsobaricItem()
where null != item
select item).ToList();
zgcGraph.InitMasterPanel(g, validItems.Count, title, this.pl);
for (int i = 0; i < validItems.Count; i++)
{
new ZedGraphScanITraq(zgcGraph, zgcGraph.MasterPane[i], false).Update(sender, new UpdateQuantificationItemEventArgs(null, validItems[i]));
}
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
panel.ClearData();
var summary = e.Item as IsobaricItem;
if (null != summary)
{
var pplData = new PointPairList();
if (summary.RawPeaks.Count > 0)
{
foreach (var peak in summary.RawPeaks)
{
pplData.Add(new PointPair(peak.Mz, peak.Intensity));
}
}
else
{
var definitions = summary.Definition.Items;
foreach (var def in definitions)
{
pplData.Add(new PointPair(def.Index, summary[def.Index]));
}
}
panel.AddIndividualLine("", pplData, Color.Black);
panel.XAxis.Scale.Min = summary.Definition.MinIndex - 1;
panel.XAxis.Scale.Max = summary.Definition.MaxIndex + 1;
panel.Title.Text = string.Format("{0},{1}", summary.Experimental, summary.Scan);
}
if (updateGraph)
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.ClearData();
try
{
var lightCorrel = new PointPairList();
foreach (var entry in summary.ObservedEnvelopes)
{
lightCorrel.Add(new PointPair(entry.Scan, entry.LightCorrelation));
}
var heavyCorrel = new PointPairList();
foreach (var entry in summary.ObservedEnvelopes)
{
heavyCorrel.Add(new PointPair(entry.Scan, entry.HeavyCorrelation));
}
var sampleCorrel = summary.SampleIsLight ? lightCorrel : heavyCorrel;
var refCorrel = summary.SampleIsLight ? heavyCorrel : lightCorrel;
panel.AddCurve("Sample", sampleCorrel, SilacQuantificationConstants.SAMPLE_COLOR, SymbolType.None);
panel.AddCurve("Reference", refCorrel, SilacQuantificationConstants.REFERENCE_COLOR, SymbolType.None);
panel.YAxis.Scale.Min = 0.0;
panel.YAxis.Scale.Max = 1.2;
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
scanItraq.Update(sender, e);
isolationWindow.Update(sender, e);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
zgcProfiles.Update(e.Item as SilacQuantificationSummaryItem);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.ClearData();
var pplO16 = new PointPairList();
var pplO18_1 = new PointPairList();
var pplO18_2 = new PointPairList();
var pplO16Curve = new PointPairList();
var pplO18_1Curve = new PointPairList();
var pplO18_2Curve = new PointPairList();
var identified = new PointPairList();
var currentScan = new PointPairList();
bool bChecked = false;
for (int i = 0; i < summary.ObservedEnvelopes.Count; i++)
{
var envelope = summary.ObservedEnvelopes[i];
if (envelope.Enabled != bChecked)
{
if (pplO16Curve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplO16Curve, O18QuantificationConstants.COLOR_O16, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_1Curve, O18QuantificationConstants.COLOR_O18_1, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_2Curve, O18QuantificationConstants.COLOR_O18_2, new[] { O18QuantificationConstants.COLOR_PLOY });
}
}
pplO16Curve = new PointPairList();
pplO18_1Curve = new PointPairList();
pplO18_2Curve = new PointPairList();
bChecked = envelope.Enabled;
}
pplO16.Add(envelope.Scan, envelope[0].Intensity);
pplO18_1.Add(envelope.Scan, envelope[2].Intensity);
pplO18_2.Add(envelope.Scan, envelope[4].Intensity);
pplO16Curve.Add(envelope.Scan, envelope[0].Intensity);
pplO18_1Curve.Add(envelope.Scan, envelope[2].Intensity);
pplO18_2Curve.Add(envelope.Scan, envelope[4].Intensity);
if (envelope.IsIdentified)
{
identified.Add(envelope.Scan, new double[] { envelope[0].Intensity, envelope[2].Intensity, envelope[4].Intensity }.Max());
}
if (envelope.IsSelected)
{
currentScan.Add(envelope.Scan, new double[] { envelope[0].Intensity, envelope[2].Intensity, envelope[4].Intensity }.Max());
}
}
if (pplO16Curve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplO16Curve, O18QuantificationConstants.COLOR_O16, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_1Curve, O18QuantificationConstants.COLOR_O18_1, new[] { O18QuantificationConstants.COLOR_PLOY });
panel.AddPoly("", pplO18_2Curve, O18QuantificationConstants.COLOR_O18_2, new[] { O18QuantificationConstants.COLOR_PLOY });
}
}
panel.AddCurve("O16", pplO16, O18QuantificationConstants.COLOR_O16, SymbolType.None);
panel.AddCurve("O18(1)", pplO18_1, O18QuantificationConstants.COLOR_O18_1, SymbolType.None);
panel.AddCurve("O18(2)", pplO18_2, O18QuantificationConstants.COLOR_O18_2, SymbolType.None);
panel.AddIndividualLine("Identified", identified, O18QuantificationConstants.COLOR_IDENTIFIED);
panel.AddIndividualLine("CurrentScan", currentScan, Color.Black);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
ITraqProteinStatisticOption option = e.Option as ITraqProteinStatisticOption;
IIdentifiedProteinGroup protein = null;
if (e.Item is IEnumerable <IIdentifiedSpectrum> )
{
var spectra = e.Item as IEnumerable <IIdentifiedSpectrum>;
protein = new IdentifiedProteinGroup();
protein.Add(new IdentifiedProtein());
protein[0].Peptides.AddRange(from s in spectra select s.Peptide);
}
else if (e.Item is IIdentifiedProteinGroup)
{
protein = e.Item as IIdentifiedProteinGroup;
}
if (protein == null)
{
throw new ArgumentException("e.Item should be IIdentifiedProteinGroup or IEnumerable<IIdentifiedSpectrum>");
}
var validItem = protein[0].Peptides.FirstOrDefault(m =>
{
var item = m.Spectrum.FindIsobaricItem();
return(null != item && item.Valid);
});
if (null == validItem)
{
zgcGraph.ClearData(true);
return;
}
var masterPane = zgcGraph.InitMasterPanel(g, 1, title, this.pl);
var panel = masterPane[0];
var samples = option.GetSamples(validItem.Spectrum.FindIsobaricItem().PlexType);
var dsNames = option.DatasetMap.Keys.OrderBy(m => m).ToList();
var ratioCalc = option.GetRatioCalculator();
List <string> xlabels = new List <string>();
List <PointPairList> outliers = new List <PointPairList>();
List <PointPairList> normals = new List <PointPairList>();
PointPairList proteins = new PointPairList();
//按照数据集循环
foreach (var dsName in dsNames)
{
var expNames = new HashSet <string>(option.DatasetMap[dsName]);
//按照样品循环
foreach (var sample in samples)
{
ratioCalc.GetSample = sample.GetValue;
ratioCalc.DatasetName = dsName;
ratioCalc.ChannelName = sample.ChannelRatioName;
ratioCalc.Filter = m => expNames.Contains(m.Query.FileScan.Experimental);
var ratios = ratioCalc.Calculate(protein);
//添加相应的分类名
xlabels.Add(dsName + ":" + sample.Name);
//每个分类有三种数据：outlier,normal和proteinratio
var outlier = new PointPairList();
outliers.Add(outlier);
var normal = new PointPairList();
normals.Add(normal);
if (ratios.Count > 0)
{
var ratio = protein[0].FindITraqChannelItem(dsName, sample.ChannelRatioName).Ratio;
proteins.Add(new PointPair()
{
Y = Math.Log(ratio)
});
ratios.ForEach(m =>
{
if (m.IsOutlier)
{
outlier.Add(new PointPair()
{
Y = Math.Log(m.Ratio)
});
}
else
{
normal.Add(new PointPair()
{
Y = Math.Log(m.Ratio)
});
}
});
}
else
{
//缺失值用missing表示。
proteins.Add(new PointPair()
{
Y = PointPair.Missing
});
}
}
}
panel.AddPoints(proteins, Color.Red, "Ratio");
AddOrdinalPoints(outliers, panel, Color.Green, "Outlier");
AddOrdinalPoints(normals, panel, Color.Black, "");
panel.XAxis.Type = AxisType.Text;
panel.XAxis.Scale.FontSpec.Angle = 90;
panel.XAxis.Scale.TextLabels = xlabels.ToArray();
panel.YAxis.Title.Text = "log(Ratio)";
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
zgcScan.Update(sender, e);
zgcPPM.Update(sender, e);
zgcCorrelation.Update(sender, e);
}
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 void Update(object sender, UpdateQuantificationItemEventArgs e)
{
ITraqProteinStatisticOption option = e.Option as ITraqProteinStatisticOption;
IIdentifiedProteinGroup protein = null;
if (e.Item is IEnumerable <IIdentifiedSpectrum> )
{
var spectra = e.Item as IEnumerable <IIdentifiedSpectrum>;
protein = new IdentifiedProteinGroup();
protein.Add(new IdentifiedProtein());
protein[0].Peptides.AddRange(from s in spectra select s.Peptide);
}
else if (e.Item is IIdentifiedProteinGroup)
{
protein = e.Item as IIdentifiedProteinGroup;
}
if (protein == null)
{
throw new ArgumentException("e.Item should be IIdentifiedProteinGroup or IEnumerable<IIdentifiedSpectrum>");
}
var validItem = protein[0].Peptides.FirstOrDefault(m =>
{
var item = m.Spectrum.FindIsobaricItem();
return(null != item && item.Valid);
});
if (null == validItem)
{
zgcGraph.ClearData(true);
return;
}
var masterPane = zgcGraph.InitMasterPanel(g, 1, title, this.pl);
var panel = masterPane[0];
var samples = option.GetSamples(validItem.Spectrum.FindIsobaricItem().PlexType);
var dsNames = option.DatasetMap.Keys.OrderBy(m => m).ToList();
var ratioCalc = option.GetRatioCalculator();
xlabels.Clear();
double index = 0.0;
string outlierStr = "Outlier";
string proteinStr = "Protein Ratio";
foreach (var dsName in dsNames)
{
var expNames = new HashSet <string>(option.DatasetMap[dsName]);
foreach (var sample in samples)
{
index += 1.0;
ratioCalc.GetSample = sample.GetValue;
ratioCalc.DatasetName = dsName;
ratioCalc.ChannelName = sample.ChannelRatioName;
ratioCalc.Filter = m => expNames.Contains(m.Query.FileScan.Experimental);
var ratios = ratioCalc.Calculate(protein);
xlabels.Add(dsName + ":" + sample.Name);
if (ratios.Count > 0)
{
var ratio = protein[0].FindITraqChannelItem(dsName, sample.ChannelRatioName).Ratio;
PointPairList pplNormal = new PointPairList();
PointPairList pplOutlier = new PointPairList();
PointPairList pplProteinRatio = new PointPairList();
foreach (var r in ratios)
{
if (r.IsOutlier)
{
pplOutlier.Add(new PointPair(index, Math.Log(r.Ratio)));
}
else
{
pplNormal.Add(new PointPair(index, Math.Log(r.Ratio)));
}
}
pplProteinRatio.Add(new PointPair(index, Math.Log(ratio)));
panel.AddPoints(pplProteinRatio, Color.Red, proteinStr);
if (pplOutlier.Count > 0)
{
panel.AddPoints(pplOutlier, Color.Green, outlierStr);
outlierStr = string.Empty;
}
panel.AddPoints(pplNormal, Color.Black);
proteinStr = string.Empty;
}
}
}
panel.XAxis.ScaleFormatEvent += new Axis.ScaleFormatHandler(XAxis_ScaleFormatEvent);
panel.XAxis.Scale.Min = 0.0;
panel.XAxis.Scale.Max = index + 1.0;
panel.XAxis.Scale.FontSpec.Angle = 90;
panel.YAxis.Title.Text = "log(Ratio)";
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
updates.Update(sender, e);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
double minMz = envelope.Light[0].Mz - 1.0;
double maxMz = envelope.Heavy[envelope.Heavy.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var pplLight = new PointPairList();
envelope.Light.ForEach(p => pplLight.Add(p.Mz, p.Intensity));
var pplHeavy = new PointPairList();
envelope.Heavy.ForEach(p => pplHeavy.Add(p.Mz, p.Intensity));
if (summary.SampleIsLight)
{
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Sample", pplLight, SilacQuantificationConstants.SAMPLE_COLOR, false);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Reference", pplHeavy, SilacQuantificationConstants.REFERENCE_COLOR, false);
}
else
{
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Sample", pplHeavy, SilacQuantificationConstants.SAMPLE_COLOR, false);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "Reference", pplLight, SilacQuantificationConstants.REFERENCE_COLOR, false);
}
// Shift the text items up by 5 user scale units above the bars
const float shift = 5;
var ppl = new PointPairList();
ppl.AddRange(pplLight);
ppl.AddRange(pplHeavy);
for (int i = 0; i < ppl.Count; i++)
{
// format the label string to have 1 decimal place
string lab = ppl[i].X.ToString("0.00");
// create the text item (assumes the x axis is ordinal or text)
// for negative bars, the label appears just above the zero value
var text = new TextObj(lab, ppl[i].X, ppl[i].Y + shift);
// tell Zedgraph to use user scale units for locating the TextItem
text.Location.CoordinateFrame = CoordType.AxisXYScale;
// AlignH the left-center of the text to the specified point
text.Location.AlignH = AlignH.Left;
text.Location.AlignV = AlignV.Center;
text.FontSpec.Border.IsVisible = false;
text.FontSpec.Fill.IsVisible = false;
// rotate the text 90 degrees
text.FontSpec.Angle = 90;
// add the TextItem to the list
zgcGraph.GraphPane.GraphObjList.Add(text);
}
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = new RawFileImpl(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Open(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.Light.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
pplRaw.Add(minMz, 0.0);
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
pplRaw.Add(maxMz, 0.0);
ZedGraphicExtension.AddIndividualLine(zgcGraph, "PeakList From RawFile", pplRaw, SilacQuantificationConstants.IDENTIFIED_COLOR, true);
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
double sampleMz;
double referenceMz;
if (summary.SampleIsLight)
{
sampleMz = summary.ObservedEnvelopes[0].Light[0].Mz;
referenceMz = summary.ObservedEnvelopes[0].Heavy[0].Mz;
}
else
{
sampleMz = summary.ObservedEnvelopes[0].Heavy[0].Mz;
referenceMz = summary.ObservedEnvelopes[0].Light[0].Mz;
}
panel.ClearData();
var pplSample = new PointPairList();
var pplReference = new PointPairList();
var pplSampleCurve = new PointPairList();
var pplReferenceCurve = new PointPairList();
bool bChecked = false;
for (int i = 0; i < summary.ObservedEnvelopes.Count; i++)
{
var envelope = summary.ObservedEnvelopes[i];
if (envelope.Enabled != bChecked)
{
if (pplSampleCurve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplSampleCurve, SilacQuantificationConstants.SAMPLE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
panel.AddPoly("", pplReferenceCurve, SilacQuantificationConstants.REFERENCE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
}
}
pplSampleCurve = new PointPairList();
pplReferenceCurve = new PointPairList();
bChecked = envelope.Enabled;
}
if (summary.SampleIsLight)
{
pplSampleCurve.Add(envelope.Scan, envelope.LightIntensity);
pplReferenceCurve.Add(envelope.Scan, envelope.HeavyIntensity);
pplSample.Add(envelope.Scan, envelope.LightIntensity);
pplReference.Add(envelope.Scan, envelope.HeavyIntensity);
}
else
{
pplSampleCurve.Add(envelope.Scan, envelope.LightIntensity);
pplReferenceCurve.Add(envelope.Scan, envelope.HeavyIntensity);
pplSample.Add(envelope.Scan, envelope.HeavyIntensity);
pplReference.Add(envelope.Scan, envelope.LightIntensity);
}
}
if (pplSampleCurve.Count > 0)
{
if (bChecked)
{
panel.AddPoly("", pplSampleCurve, SilacQuantificationConstants.SAMPLE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
panel.AddPoly("", pplReferenceCurve, SilacQuantificationConstants.REFERENCE_COLOR, new[] { SilacQuantificationConstants.PLOY_COLOR });
}
}
panel.AddCurve("Sample", pplSample, SilacQuantificationConstants.SAMPLE_COLOR, SymbolType.None);
panel.AddCurve("Reference", pplReference, SilacQuantificationConstants.REFERENCE_COLOR, SymbolType.None);
var identified = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsIdentified).ForEach(m =>
{
identified.Add(new PointPair(m.Scan, m.LightIntensity));
identified.Add(new PointPair(m.Scan, m.HeavyIntensity));
});
panel.AddIndividualLine("Identified", identified, SilacQuantificationConstants.IDENTIFIED_COLOR);
var currentScan = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsSelected).ForEach(m =>
{
currentScan.Add(new PointPair(m.Scan, Math.Max(m.LightIntensity, m.HeavyIntensity)));
});
if (currentScan.Count > 0)
{
panel.AddIndividualLine("CurrentScan", currentScan, Color.Black);
}
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var summary = e.Item as SilacQuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.ClearData();
try
{
int firstScan = summary.ObservedEnvelopes.First().Scan;
int lastScan = summary.ObservedEnvelopes.Last().Scan;
var samplePPMList = summary.GetSamplePPMList();
var refPPMList = summary.GetReferencePPMList();
var samplePPMs = GetPoints(firstScan, lastScan, samplePPMList);
var referencePPMs = GetPoints(firstScan, lastScan, refPPMList);
panel.AddCurve("Sample", samplePPMs, SilacQuantificationConstants.SAMPLE_COLOR, SymbolType.None);
panel.AddCurve("Reference", referencePPMs, SilacQuantificationConstants.REFERENCE_COLOR, SymbolType.None);
var identified = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsIdentified).ForEach(m =>
{
if (samplePPMList.ContainsKey(m))
{
identified.Add(new PointPair(m.Scan, samplePPMList[m]));
}
if (refPPMList.ContainsKey(m))
{
identified.Add(new PointPair(m.Scan, refPPMList[m]));
}
});
panel.AddIndividualLine("Identified", identified, SilacQuantificationConstants.IDENTIFIED_COLOR);
var selected = new PointPairList();
summary.ObservedEnvelopes.FindAll(m => m.IsSelected).ForEach(m =>
{
if (samplePPMList.ContainsKey(m))
{
selected.Add(new PointPair(m.Scan, samplePPMList[m]));
}
if (refPPMList.ContainsKey(m))
{
selected.Add(new PointPair(m.Scan, refPPMList[m]));
}
});
if (selected.Count > 0)
{
panel.AddIndividualLine("CurrentScan", selected, Color.Black);
}
panel.YAxis.Scale.Min = -10;
panel.YAxis.Scale.Max = 10;
}
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)
{
var summary = e.Item as O18QuantificationSummaryItem;
if (summary == null)
{
throw new ArgumentNullException("UpdateQuantificationItemEventArgs.Item cannot be null");
}
panel.InitGraphPane(this.title, "m/z", "Intensity", true, 0.0);
ZedGraphicExtension.ClearData(zgcGraph, false);
try
{
var envelope = summary.ObservedEnvelopes.Find(m => m.IsSelected);
if (envelope == null)
{
return;
}
panel.InitGraphPane(this.title + ", Scan=" + envelope.Scan.ToString(), "m/z", "Intensity", true, 0.0);
double minMz = envelope[0].Mz - 1.0;
double maxMz = envelope[envelope.Count - 1].Mz + 1.0;
zgcGraph.GraphPane.XAxis.Scale.Min = minMz;
zgcGraph.GraphPane.XAxis.Scale.Max = maxMz;
var ppl = new PointPairList();
envelope.ForEach(p => { if (p.Intensity > 0)
{
ppl.Add(p.Mz, p.Intensity);
}
});
panel.AddIndividualLine("Isotopic Envelope", ppl, Color.Red);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
var halfMax = (from env in envelope
select env.Intensity).Max() / 2;
ppl.Clear();
envelope.ForEach(p => { if (p.Intensity == 0)
{
ppl.Add(p.Mz, halfMax);
}
});
panel.AddIndividualLine("", ppl, defaultColor: Color.Red, dStyle: DashStyle.Dash);
panel.AddTextUp(ppl, 5, (m => m.X.ToString("0.0000")));
if (File.Exists(summary.RawFilename))
{
if (rawFile == null)
{
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
else if (!rawFile.FileName.Equals(summary.RawFilename))
{
rawFile.Close();
rawFile = RawFileFactory.GetRawFileReader(summary.RawFilename);
}
PeakList <Peak> pkl = rawFile.GetPeakList(envelope.ScanTimes[0].Scan);
var pplRaw = new PointPairList();
for (int i = 0; i < pkl.Count; i++)
{
if (pkl[i].Mz < minMz)
{
continue;
}
else if (pkl[i].Mz > maxMz)
{
break;
}
pplRaw.Add(pkl[i].Mz, -pkl[i].Intensity);
}
panel.AddIndividualLine("PeakList From RawFile", pplRaw, Color.Blue);
panel.AddTextDown(pplRaw, 5, (m => m.X.ToString("0.0000")));
/*
* foreach (var p in ppl)
* {
* if (p.Y == 0)
* {
* double ppm = double.MaxValue;
* double ppmAbs = Math.Abs(ppm);
* foreach (var pp in pplRaw)
* {
* double ppmCur = PrecursorUtils.mz2ppm(pp.X, pp.X - p.X);
* double ppmCurAbs = Math.Abs(ppmCur);
* if (Math.Abs(ppmCur) < ppmAbs)
* {
* ppm = ppmCur;
* ppmAbs = ppmCurAbs;
* }
*
* if (pp.X > p.X)
* {
* break;
* }
* }
*
* p.Z = ppm;
* }
* }
*/
}
}
finally
{
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
}
