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 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);
}
public ZedGraphO18Experimental_ScanPPM(ZedGraphControl zgcGraph, Graphics g)
{
MasterPane myMaster = ZedGraphicExtension.InitMasterPanel(zgcGraph, g, 2, "Experimental Envelopes");
updates.Updates.Add(new ZedGraphO18ExperimentalScan(zgcGraph, myMaster.PaneList[0], ""));
updates.Updates.Add(new ZedGraphO18ExperimentalPPM(zgcGraph, myMaster.PaneList[1], ""));
}
public ZedGraphExperimentalCorrelation(ZedGraphControl zgcGraph, GraphPane panel, string title)
{
this.zgcGraph = zgcGraph;
this.panel = panel;
panel.InitGraphPane(title, "Scan", "Cosine similarity", true, 0.0);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public ZedGraphMRMProductIonScans(ZedGraphControl zgcGraph, GraphPane panel)
{
this.zgcGraph = zgcGraph;
this.panel = panel;
panel.InitGraphPane(null, "Retention Time", "Ion Count", true, 0.0);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
private void zgcProtein_MouseDoubleClick(object sender, MouseEventArgs e)
{
var mph = ZedGraphicExtension.GetObject(sender as ZedGraphControl, e) as IIdentifiedSpectrum;
if (null != mph)
{
ShowPeptideInfo(mph);
}
}
public ZedGraphMRMRegression(ZedGraphControl zgcGraph, GraphPane panel)
{
this.zgcGraph = zgcGraph;
this.panel = panel;
panel.InitGraphPane(null, "Heavy intensity", "Light intensity", true, 0.0);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public ZedGraphScanIsolationWindow(ZedGraphControl zgcGraph, GraphPane panel)
{
this.zgcGraph = zgcGraph;
this.panel = panel;
panel.InitGraphPane("Isolation Window", "m/z", "Intensity", true, 0.0);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public ZedGraphScanITraq(ZedGraphControl zgcGraph, GraphPane panel, bool updateGraph)
{
this.zgcGraph = zgcGraph;
this.panel = panel;
this.updateGraph = updateGraph;
panel.InitGraphPane("Isobaric Tag Channels", "m/z", "Intensity", true, 0.0);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public ZedGraphSmallMoleculeFilePeak(ZedGraphControl zgcGraph, GraphPane panel, string title, Color color)
{
this.zgcGraph = zgcGraph;
this.panel = panel;
this.color = color;
panel.InitGraphPane(title, "Scan", "Intensity", true, 0.0);
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");
}
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, UpdateMRMPairedProductIonEventArgs e)
{
var summary = e.Item;
if (summary == null)
{
throw new ArgumentNullException("UpdateMRMItemEventArgs.Item cannot be null");
}
panel.Tag = e.Item;
panel.ClearData();
try
{
if (summary.Heavy != null)
{
var pplRed = new PointPairList();
var noise = summary.DeductBaseLine ? summary.Light.Noise : 0.0;
for (int i = 0; i < summary.Light.Intensities.Count; i++)
{
if (summary.Light.Intensities[i].Enabled)
{
pplRed.Add(new PointPair(summary.Heavy.Intensities[i].Intensity - noise, summary.Light.Intensities[i].Intensity - noise, 0.0, i));
}
}
;
if (pplRed.Count > 0)
{
panel.AddPoints(pplRed, Color.Red);
PointPairList line = ZedGraphicExtension.GetRegressionLine(pplRed, summary.Ratio, summary.Distance);
panel.AddCurve(null, line, Color.Green, SymbolType.None);
panel.Title.Text = summary.GetFormula();
panel.Title.IsVisible = true;
}
else
{
panel.Title.IsVisible = false;
}
}
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
public void Update(object sender, UpdateMRMPairedPeptideItemEventArgs e)
{
MasterPane myMaster = zgcGraph.MasterPane;
myMaster.Border.IsVisible = false;
myMaster.PaneList.Clear();
try
{
myMaster.Margin.All = 1;
myMaster.InnerPaneGap = 1;
myMaster.Title.IsVisible = false;
myMaster.Legend.IsVisible = false;
var summary = e.Item;
if (summary == null)
{
return;
}
for (int i = 0; i < summary.ProductIonPairs.Count; i++)
{
if (summary.ProductIonPairs[i] == null)
{
continue;
}
if (string.IsNullOrEmpty(FileName) || FileName.Equals(summary.ProductIonPairs[i].FileName))
{
GraphPane panel = new GraphPane();
myMaster.Add(panel);
ZedGraphMRMProductIonScans scan = new ZedGraphMRMProductIonScans(zgcGraph, panel);
scan.Update(null, new UpdateMRMPairedProductIonEventArgs(summary.ProductIonPairs[i], e.ViewOption));
}
}
myMaster.SetLayout(g, PaneLayout.SquareColPreferred);
zgcGraph.AxisChange();
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
public void Update(object sender, UpdateSmallMoleculeFilePeakEventArgs e)
{
var peak = e.Peak;
panel.ClearData();
var pplReal = new PointPairList();
var pplSmoothed = new PointPairList();
var map = data[peak];
foreach (var scan in map)
{
pplReal.Add(scan.Scan, scan.Intensity);
pplSmoothed.Add(scan.Scan, scan.SmoothedIntensity);
}
if (map.Last().Scan != LastScan)
{
pplReal.Add(LastScan, 0.0);
}
panel.YAxis.Scale.MaxAuto = true;
bool bSmoothed = false;
foreach (var m in map)
{
if (m.Intensity != m.SmoothedIntensity)
{
bSmoothed = true;
break;
}
}
if (bSmoothed)
{
var line = panel.AddCurve("", pplSmoothed, Color.Blue, SymbolType.None);
}
panel.AddCurve("", pplReal, this.color, SymbolType.None);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateMRMPairedPeptideItemEventArgs e)
{
MasterPane myMaster = zgcGraph.MasterPane;
myMaster.Border.IsVisible = false;
myMaster.PaneList.Clear();
bool updated = false;
try
{
myMaster.Margin.All = 1;
myMaster.InnerPaneGap = 1;
myMaster.Title.IsVisible = false;
myMaster.Legend.IsVisible = false;
var summary = e.Item;
if (summary == null)
{
return;
}
var ion = summary.ProductIonPairs.FirstOrDefault(m => m != null && m.FileName.Equals(FileName));
if (ion == null)
{
return;
}
ZedGraphMRMProductIonScansAndRegression scan = new ZedGraphMRMProductIonScansAndRegression(zgcGraph, g);
scan.Update(null, new UpdateMRMPairedProductIonEventArgs(ion, e.ViewOption));
updated = true;
}
finally
{
if (!updated)
{
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, UpdateMRMPairedProductIonEventArgs e)
{
var summary = e.Item;
if (summary == null)
{
throw new ArgumentNullException("UpdateMRMPairedProductIonEventArgs.Item cannot be null");
}
MasterPane myMaster = zgcGraph.MasterPane;
myMaster.Border.IsVisible = false;
myMaster.PaneList.Clear();
try
{
myMaster.Margin.All = 10;
myMaster.InnerPaneGap = 10;
// Set the master pane title
myMaster.Title.Text = MyConvert.Format("{0:0.0000} - {1:0.0000}", summary.Light == null ? 0.0 : summary.Light.PrecursorMZ, summary.Heavy == null ? 0.0 : summary.Heavy.PrecursorMZ);
myMaster.Title.IsVisible = true;
myMaster.Legend.IsVisible = false;
myMaster.Add(new GraphPane());
myMaster.Add(new GraphPane());
new ZedGraphMRMProductIonScans(zgcGraph, myMaster.PaneList[0]).Update(null, e);
new ZedGraphMRMRegression(zgcGraph, myMaster.PaneList[1]).Update(null, e);
myMaster.SetLayout(g, PaneLayout.SingleRow);
zgcGraph.AxisChange();
}
finally
{
ZedGraphicExtension.UpdateGraph(this.zgcGraph);
}
}
