protected override void Recalc()
{
cbxAutoFindPeak.Checked = PeptideFileAnalysis.AutoFindPeak;
cbxSmooth.Checked = Smooth;
MsGraphControl.GraphPane.GraphObjList.Clear();
MsGraphControl.GraphPane.CurveList.Clear();
_peakLines = null;
if (!PeptideFileAnalysis.IsMzKeySetComplete(PeptideFileAnalysis.ChromatogramSet.Chromatograms.Keys))
{
return;
}
var overlayFileAnalysis = UpdateDataFileCombo(comboOverlay);
var peakLines = new Dictionary <TracerFormula, PeakDisplay>();
var tracerChromatograms = GetPoints();
TracerChromatograms overlayTracerChromatograms = null;
double[] mappedTimes = null;
if (overlayFileAnalysis != null)
{
overlayTracerChromatograms = overlayFileAnalysis.GetTracerChromatograms(Smooth);
var retentionTimeAlignment =
overlayFileAnalysis.MsDataFile.GetRetentionTimeAlignment(PeptideFileAnalysis.MsDataFile);
mappedTimes =
overlayTracerChromatograms.Times.Select(retentionTimeAlignment.GetTargetTime).ToArray();
}
var peaks = PeptideFileAnalysis.CalculatedPeaks;
var entries = tracerChromatograms.Points.ToArray();
if (dataGridView1.Rows.Count != entries.Length)
{
dataGridView1.Rows.Clear();
dataGridView1.Rows.Add(entries.Length);
}
if (cbxShowScore.Checked)
{
var scoreLine = MsGraphControl.GraphPane.AddCurve("Score", tracerChromatograms.Times.ToArray(), tracerChromatograms.Scores.ToArray(), Color.Black, SymbolType.None);
scoreLine.IsY2Axis = true;
scoreLine.Line.Width = Settings.Default.ChromatogramLineWidth;
}
double totalAmount = peaks.Peaks.Values.Sum(p => p.Area);
double totalSlope = peaks.Peaks.Values.Sum(p => p.RatioToBase);
for (int iCandidate = 0; iCandidate < entries.Count(); iCandidate++)
{
var entry = entries[iCandidate];
var label = entry.Key.ToDisplayString();
var row = dataGridView1.Rows[iCandidate];
row.Cells[colFormula.Index].Value = label;
var peak = peaks.GetPeak(entry.Key);
if (peak != null)
{
row.Cells[colAreaPct.Index].Value = peak.Value.Area / totalAmount;
row.Cells[colSlopePct.Index].Value = peak.Value.RatioToBase / totalSlope;
row.Cells[colStartTime.Index].Value = peak.Value.StartTime;
row.Cells[colEndTime.Index].Value = peak.Value.EndTime;
row.Cells[colArea.Index].Value = peak.Value.Area;
row.Cells[colCorr.Index].Value = peak.Value.Correlation;
}
else
{
row.Cells[colAreaPct.Index].Value = null;
row.Cells[colStartTime.Index].Value = null;
row.Cells[colEndTime.Index].Value = null;
row.Cells[colArea.Index].Value = null;
row.Cells[colCorr.Index].Value = null;
}
row.Cells[colFormula.Index].Style.BackColor = row.Cells[colAreaPct.Index].Style.BackColor
= GetColor(iCandidate, entries.Length);
row.Tag = entry.Key;
if (IsDisplayed(entry.Key))
{
var curve = new ChromatogramGraphItem
{
Title = label,
Color = GetColor(iCandidate, entries.Length),
Points = new PointPairList(tracerChromatograms.Times, entry.Value),
};
var chromCurveItem = (LineItem)MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, curve);
chromCurveItem.Label.IsVisible = false;
chromCurveItem.Line.Width = Settings.Default.ChromatogramLineWidth;
if (overlayTracerChromatograms != null)
{
var overlayCurve = new ChromatogramGraphItem
{
Title = overlayFileAnalysis.MsDataFile.Label + " " + label,
Color = GetColor(iCandidate, entries.Length),
Points =
new PointPairList(mappedTimes,
overlayTracerChromatograms.Points[entry.Key])
};
var overlayCurveItem = (LineItem)MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, overlayCurve);
overlayCurveItem.Label.IsVisible = false;
overlayCurveItem.Line.Style = DashStyle.Dash;
overlayCurveItem.Line.Width = Settings.Default.ChromatogramLineWidth;
}
if (peak != null)
{
var peakDisplay = new PeakDisplay();
var color = GetColor(iCandidate, entries.Length);
var max = MaxInRange(entry.Value, tracerChromatograms.ChromatogramSet.IndexFromTime(peak.Value.StartTime),
tracerChromatograms.ChromatogramSet.IndexFromTime(peak.Value.EndTime));
peakDisplay.Start = peak.Value.StartTime;
peakDisplay.End = peak.Value.EndTime;
peakDisplay.Height = max;
if (PeaksAsHorizontalLines)
{
peakDisplay.HorizontalLine = MsGraphControl.GraphPane.AddCurve(null, new[] { peakDisplay.Start, peakDisplay.End }, new[] { max, max }, color);
peakDisplay.HorizontalLine.Line.Width = Settings.Default.ChromatogramLineWidth;
}
if (PeaksAsVerticalLines)
{
peakDisplay.StartVerticalLine = MsGraphControl.GraphPane.AddCurve(
null,
new[] { peakDisplay.Start, peakDisplay.Start },
new[] { max, 0 }, color, SymbolType.None
);
peakDisplay.StartVerticalLine.Line.Width = Settings.Default.ChromatogramLineWidth;
peakDisplay.EndVerticalLine = MsGraphControl.GraphPane.AddCurve(
null,
new[] { peakDisplay.End, peakDisplay.End },
new[] { max, 0 }, color, SymbolType.None
);
peakDisplay.EndVerticalLine.Line.Width = Settings.Default.ChromatogramLineWidth;
}
peakLines.Add(entry.Key, peakDisplay);
}
}
}
// foreach (var peakSet in tracerChromatograms.GetNonOverlappingPeakSets())
// {
// double start = PeptideFileAnalysis.TimeFromScanIndex(peakSet.StartIndex);
// double end = PeptideFileAnalysis.TimeFromScanIndex(peakSet.EndIndex);
// double rawScore = tracerChromatograms.GetScore(peakSet.StartIndex, peakSet.EndIndex);
// double colorScore = Math.Pow(rawScore, 4);
// var color = Color.FromArgb((int) (255 - (255*colorScore)), (int) (255*colorScore), 0);
// var box = new BoxObj(start, int.MaxValue, end - start, int.MaxValue, Color.Black, color)
// {
// IsClippedToChartRect = true,
// ZOrder = ZOrder.F_BehindGrid,
// };
// msGraphControl.GraphPane.GraphObjList.Add(box);
// double retentionTime = tracerChromatograms.Times[peakSet.BestRetentionTime];
// double intensity = tracerChromatograms.GetMaxIntensity(peakSet);
// var textObj = new TextObj(retentionTime.ToString("0.##"), retentionTime,
// intensity, CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
// {
// FontSpec = {Fill = new Fill(color),},
// Tag = peakSet,
// };
// msGraphControl.GraphPane.GraphObjList.Add(textObj);
// }
if (PeptideFileAnalysis.PsmTimes != null)
{
foreach (var time in PeptideFileAnalysis.PsmTimes.SelectMany(entry => entry.Value))
{
MsGraphControl.GraphPane.GraphObjList.Add(new LineObj(Color.LightBlue, time, 0, time,
1)
{
Line = { Style = DashStyle.DashDot },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
});
}
}
else
{
var otherPeaks = PeptideAnalysis.FileAnalyses.Select(f => f.CalculatedPeaks);
double firstDetectedTime, lastDetectedTime;
PeptideFileAnalysis.CalculatedPeaks.GetFirstLastTimes(otherPeaks, out firstDetectedTime, out lastDetectedTime);
MsGraphControl.GraphPane.GraphObjList.Add(new LineObj(Color.Black, firstDetectedTime, 0,
firstDetectedTime, 1)
{
Line = { Style = DashStyle.DashDotDot },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
});
MsGraphControl.GraphPane.GraphObjList.Add(new LineObj(Color.Black, lastDetectedTime, 0,
lastDetectedTime, 1)
{
Line = { Style = DashStyle.DashDotDot },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
});
}
MsGraphControl.AxisChange();
MsGraphControl.Invalidate();
_peakLines = peakLines;
tbxTracerPercentByAreas.Text = peaks.CalcTracerPercentByAreas().ToString();
tbxTracerPercentBySlopes.Text = peaks.CalcTracerPercentByRatios().ToString();
tbxScore.Text = peaks.DeconvolutionScore.ToString();
double rtShift, rtStdDev;
peaks.RetentionTimeShift(out rtShift, out rtStdDev);
var retentionTimeShift = rtShift.ToString("#.00");
if (!double.IsNaN(rtStdDev) && !double.IsInfinity(rtStdDev))
{
retentionTimeShift += "+/-" + rtStdDev.ToString("#.00");
}
tbxRetentionTimeShift.Text = retentionTimeShift;
}
protected override void Recalc()
{
cbxAutoFindPeak.Checked = PeptideFileAnalysis.AutoFindPeak;
cbxSmooth.Checked = Smooth;
MsGraphControl.GraphPane.GraphObjList.Clear();
MsGraphControl.GraphPane.CurveList.Clear();
_peakLines = null;
if (!PeptideFileAnalysis.IsMzKeySetComplete(PeptideFileAnalysis.ChromatogramSet.Chromatograms.Keys))
{
return;
}
var overlayFileAnalysis = UpdateDataFileCombo(comboOverlay);
var peakLines = new Dictionary<TracerFormula, PeakDisplay>();
var tracerChromatograms = GetPoints();
TracerChromatograms overlayTracerChromatograms = null;
double[] mappedTimes = null;
if (overlayFileAnalysis != null)
{
overlayTracerChromatograms = overlayFileAnalysis.GetTracerChromatograms(Smooth);
var retentionTimeAlignment =
overlayFileAnalysis.MsDataFile.GetRetentionTimeAlignment(PeptideFileAnalysis.MsDataFile);
mappedTimes =
overlayTracerChromatograms.Times.Select(retentionTimeAlignment.GetTargetTime).ToArray();
}
var peaks = PeptideFileAnalysis.CalculatedPeaks;
var entries = tracerChromatograms.Points.ToArray();
if (dataGridView1.Rows.Count != entries.Length)
{
dataGridView1.Rows.Clear();
dataGridView1.Rows.Add(entries.Length);
}
if (cbxShowScore.Checked)
{
var scoreLine = MsGraphControl.GraphPane.AddCurve("Score", tracerChromatograms.Times.ToArray(), tracerChromatograms.Scores.ToArray(), Color.Black, SymbolType.None);
scoreLine.IsY2Axis = true;
scoreLine.Line.Width = Settings.Default.ChromatogramLineWidth;
}
double totalAmount = peaks.Peaks.Values.Sum(p => p.Area);
double totalSlope = peaks.Peaks.Values.Sum(p => p.RatioToBase);
for (int iCandidate = 0; iCandidate < entries.Count(); iCandidate++)
{
var entry = entries[iCandidate];
var label = entry.Key.ToDisplayString();
var row = dataGridView1.Rows[iCandidate];
row.Cells[colFormula.Index].Value = label;
var peak = peaks.GetPeak(entry.Key);
if (peak != null)
{
row.Cells[colAreaPct.Index].Value = peak.Value.Area/totalAmount;
row.Cells[colSlopePct.Index].Value = peak.Value.RatioToBase/totalSlope;
row.Cells[colStartTime.Index].Value = peak.Value.StartTime;
row.Cells[colEndTime.Index].Value = peak.Value.EndTime;
row.Cells[colArea.Index].Value = peak.Value.Area;
row.Cells[colCorr.Index].Value = peak.Value.Correlation;
}
else
{
row.Cells[colAreaPct.Index].Value = null;
row.Cells[colStartTime.Index].Value = null;
row.Cells[colEndTime.Index].Value = null;
row.Cells[colArea.Index].Value = null;
row.Cells[colCorr.Index].Value = null;
}
row.Cells[colFormula.Index].Style.BackColor = row.Cells[colAreaPct.Index].Style.BackColor
= GetColor(iCandidate, entries.Length);
row.Tag = entry.Key;
if (IsDisplayed(entry.Key))
{
var curve = new ChromatogramGraphItem
{
Title = label,
Color = GetColor(iCandidate, entries.Length),
Points = new PointPairList(tracerChromatograms.Times, entry.Value),
};
var chromCurveItem = (LineItem) MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, curve);
chromCurveItem.Label.IsVisible = false;
chromCurveItem.Line.Width = Settings.Default.ChromatogramLineWidth;
if (overlayTracerChromatograms != null)
{
var overlayCurve = new ChromatogramGraphItem
{
Title = overlayFileAnalysis.MsDataFile.Label + " " + label,
Color = GetColor(iCandidate, entries.Length),
Points =
new PointPairList(mappedTimes,
overlayTracerChromatograms.Points[entry.Key])
};
var overlayCurveItem = (LineItem) MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, overlayCurve);
overlayCurveItem.Label.IsVisible = false;
overlayCurveItem.Line.Style = DashStyle.Dash;
overlayCurveItem.Line.Width = Settings.Default.ChromatogramLineWidth;
}
if (peak != null)
{
var peakDisplay = new PeakDisplay();
var color = GetColor(iCandidate, entries.Length);
var max = MaxInRange(entry.Value, tracerChromatograms.ChromatogramSet.IndexFromTime(peak.Value.StartTime),
tracerChromatograms.ChromatogramSet.IndexFromTime(peak.Value.EndTime));
peakDisplay.Start = peak.Value.StartTime;
peakDisplay.End = peak.Value.EndTime;
peakDisplay.Height = max;
if (PeaksAsHorizontalLines)
{
peakDisplay.HorizontalLine = MsGraphControl.GraphPane.AddCurve(null, new[] { peakDisplay.Start, peakDisplay.End }, new[] { max, max }, color);
peakDisplay.HorizontalLine.Line.Width = Settings.Default.ChromatogramLineWidth;
}
if (PeaksAsVerticalLines)
{
peakDisplay.StartVerticalLine = MsGraphControl.GraphPane.AddCurve(
null,
new[] { peakDisplay.Start, peakDisplay.Start },
new[] {max, 0}, color, SymbolType.None
);
peakDisplay.StartVerticalLine.Line.Width = Settings.Default.ChromatogramLineWidth;
peakDisplay.EndVerticalLine = MsGraphControl.GraphPane.AddCurve(
null,
new[] { peakDisplay.End, peakDisplay.End },
new[] { max, 0 }, color, SymbolType.None
);
peakDisplay.EndVerticalLine.Line.Width = Settings.Default.ChromatogramLineWidth;
}
peakLines.Add(entry.Key, peakDisplay);
}
}
}
// foreach (var peakSet in tracerChromatograms.GetNonOverlappingPeakSets())
// {
// double start = PeptideFileAnalysis.TimeFromScanIndex(peakSet.StartIndex);
// double end = PeptideFileAnalysis.TimeFromScanIndex(peakSet.EndIndex);
// double rawScore = tracerChromatograms.GetScore(peakSet.StartIndex, peakSet.EndIndex);
// double colorScore = Math.Pow(rawScore, 4);
// var color = Color.FromArgb((int) (255 - (255*colorScore)), (int) (255*colorScore), 0);
// var box = new BoxObj(start, int.MaxValue, end - start, int.MaxValue, Color.Black, color)
// {
// IsClippedToChartRect = true,
// ZOrder = ZOrder.F_BehindGrid,
// };
// msGraphControl.GraphPane.GraphObjList.Add(box);
// double retentionTime = tracerChromatograms.Times[peakSet.BestRetentionTime];
// double intensity = tracerChromatograms.GetMaxIntensity(peakSet);
// var textObj = new TextObj(retentionTime.ToString("0.##"), retentionTime,
// intensity, CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
// {
// FontSpec = {Fill = new Fill(color),},
// Tag = peakSet,
// };
// msGraphControl.GraphPane.GraphObjList.Add(textObj);
// }
if (PeptideFileAnalysis.PsmTimes != null)
{
foreach (var time in PeptideFileAnalysis.PsmTimes.SelectMany(entry=>entry.Value))
{
MsGraphControl.GraphPane.GraphObjList.Add(new LineObj(Color.LightBlue, time, 0, time,
1)
{
Line = { Style = DashStyle.DashDot },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
});
}
}
else
{
var otherPeaks = PeptideAnalysis.FileAnalyses.Select(f => f.CalculatedPeaks);
double firstDetectedTime, lastDetectedTime;
PeptideFileAnalysis.CalculatedPeaks.GetFirstLastTimes(otherPeaks, out firstDetectedTime, out lastDetectedTime);
MsGraphControl.GraphPane.GraphObjList.Add(new LineObj(Color.Black, firstDetectedTime, 0,
firstDetectedTime, 1)
{
Line = {Style = DashStyle.DashDotDot},
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
});
MsGraphControl.GraphPane.GraphObjList.Add(new LineObj(Color.Black, lastDetectedTime, 0,
lastDetectedTime, 1)
{
Line = { Style = DashStyle.DashDotDot },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true,
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
});
}
MsGraphControl.AxisChange();
MsGraphControl.Invalidate();
_peakLines = peakLines;
tbxTracerPercentByAreas.Text = peaks.CalcTracerPercentByAreas().ToString();
tbxTracerPercentBySlopes.Text = peaks.CalcTracerPercentByRatios().ToString();
tbxScore.Text = peaks.DeconvolutionScore.ToString();
double rtShift, rtStdDev;
peaks.RetentionTimeShift(out rtShift, out rtStdDev);
var retentionTimeShift = rtShift.ToString("#.00");
if (!double.IsNaN(rtStdDev) && !double.IsInfinity(rtStdDev))
{
retentionTimeShift += "+/-" + rtStdDev.ToString("#.00");
}
tbxRetentionTimeShift.Text = retentionTimeShift;
}
protected void ShowChromatograms()
{
if (MsGraphControl.GraphPane == null)
{
// TODO: How can this happen?
return;
}
MsGraphControl.GraphPane.GraphObjList.Clear();
MsGraphControl.GraphPane.CurveList.Clear();
var selectedCharges = gridIntensities.GetSelectedCharges();
var selectedMasses = gridIntensities.GetSelectedMasses();
var chromatograms = PeptideFileAnalysis.ChromatogramSet;
var mzRanges = PeptideFileAnalysis.TurnoverCalculator.GetMzs(0);
var monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideAnalysis.Peptide.Sequence);
for (int charge = PeptideAnalysis.MinCharge; charge <= PeptideAnalysis.MaxCharge; charge++)
{
if (selectedCharges.Count > 0 && !selectedCharges.Contains(charge))
{
continue;
}
for (int iMass = 0; iMass < PeptideAnalysis.GetMassCount(); iMass++)
{
var mzKey = new MzKey(charge, iMass);
double massDifference = mzRanges[iMass].Center - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
if (selectedMasses.Count > 0)
{
if (!selectedMasses.Contains(iMass))
{
continue;
}
}
else
{
if (ExcludedMasses.IsExcluded(mzKey.MassIndex))
{
continue;
}
}
ChromatogramSetData.Chromatogram chromatogram;
if (!chromatograms.Chromatograms.TryGetValue(mzKey, out chromatogram))
{
continue;
}
var graphItem = new ChromatogramGraphItem
{
Title = label,
};
graphItem.Color = TracerChromatogramForm.GetColor(iMass, PeptideAnalysis.GetMassCount());
var mzRange = PeptideFileAnalysis.TurnoverCalculator.GetMzs(mzKey.Charge)[mzKey.MassIndex];
var massAccuracy = PeptideAnalysis.GetMassAccuracy();
var intensities = chromatogram.ChromatogramPoints.Select(point => point.GetIntensity(mzRange, massAccuracy)).ToArray();
if (Smooth)
{
intensities = TracerChromatograms.SavitzkyGolaySmooth(intensities);
}
PointPairList points = new PointPairList(chromatograms.Times, intensities);
graphItem.Points = points;
var lineItem = (LineItem)MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, graphItem);
lineItem.Line.Style = TracerChromatogramForm.GetDashStyle(charge - PeptideAnalysis.MinCharge);
lineItem.Line.Width = Settings.Default.ChromatogramLineWidth;
lineItem.Label.IsVisible = false;
}
}
}
protected void ShowChromatograms()
{
if (MsGraphControl.GraphPane == null)
{
// TODO: How can this happen?
return;
}
MsGraphControl.GraphPane.GraphObjList.Clear();
MsGraphControl.GraphPane.CurveList.Clear();
var selectedCharges = gridIntensities.GetSelectedCharges();
var selectedMasses = gridIntensities.GetSelectedMasses();
var chromatograms = PeptideFileAnalysis.ChromatogramSet;
var mzRanges = PeptideFileAnalysis.TurnoverCalculator.GetMzs(0);
var monoisotopicMass = Workspace.GetAminoAcidFormulas().GetMonoisotopicMass(PeptideAnalysis.Peptide.Sequence);
for (int charge = PeptideAnalysis.MinCharge; charge <= PeptideAnalysis.MaxCharge; charge++)
{
if (selectedCharges.Count > 0 && !selectedCharges.Contains(charge))
{
continue;
}
for (int iMass = 0; iMass < PeptideAnalysis.GetMassCount(); iMass++)
{
var mzKey = new MzKey(charge, iMass);
double massDifference = mzRanges[iMass].Center - monoisotopicMass;
var label = massDifference.ToString("0.#");
if (label[0] != '-')
{
label = "+" + label;
}
label = "M" + label;
label += new string('+', charge);
if (selectedMasses.Count > 0)
{
if (!selectedMasses.Contains(iMass))
{
continue;
}
}
else
{
if (ExcludedMasses.IsExcluded(mzKey.MassIndex))
{
continue;
}
}
ChromatogramSetData.Chromatogram chromatogram;
if (!chromatograms.Chromatograms.TryGetValue(mzKey, out chromatogram))
{
continue;
}
var graphItem = new ChromatogramGraphItem
{
Title = label,
};
graphItem.Color = TracerChromatogramForm.GetColor(iMass, PeptideAnalysis.GetMassCount());
var mzRange = PeptideFileAnalysis.TurnoverCalculator.GetMzs(mzKey.Charge)[mzKey.MassIndex];
var massAccuracy = PeptideAnalysis.GetMassAccuracy();
var intensities = chromatogram.ChromatogramPoints.Select(point => point.GetIntensity(mzRange, massAccuracy)).ToArray();
if (Smooth)
{
intensities = TracerChromatograms.SavitzkyGolaySmooth(intensities);
}
PointPairList points = new PointPairList(chromatograms.Times, intensities);
graphItem.Points = points;
var lineItem = (LineItem)MsGraphControl.AddGraphItem(MsGraphControl.GraphPane, graphItem);
lineItem.Line.Style = TracerChromatogramForm.GetDashStyle(charge - PeptideAnalysis.MinCharge);
lineItem.Line.Width = Settings.Default.ChromatogramLineWidth;
lineItem.Label.IsVisible = false;
}
}
}