/// <summary>
/// Build the isotope plot showing theoretical isotopic profile and
/// actual isotopic profile.
/// </summary>
/// <param name="theoretical">Actual isotopic profile.</param>
/// <param name="observed">Actual isotopic profile.</param>
/// <param name="isProfile">A value indicating whether the peak list is profile mode.</param>
public void BuildPlot(PeakDataPoint[] theoretical, PeakDataPoint[] observed, bool isProfile)
{
PlotModel.Series.Clear();
// Create series for theoretical isotope profile
var theoSeries = new PeakPointSeries
{
Title = "Theoretical",
ItemsSource = theoretical,
Color = OxyColor.FromArgb(120, 0, 0, 0),
StrokeThickness = 3.0,
TrackerFormatString =
"{0}" + Environment.NewLine +
"{1}: {2:0.###}" + Environment.NewLine +
"{3}: {4:0.###}" + Environment.NewLine +
"Index: {Index:0.###}"
};
PlotModel.Series.Add(theoSeries);
if (isProfile)
{
// Create series for actual isotope profile
var actSeries = new ProfilePeakPointSeries
{
Title = "Observed",
ItemsSource = observed,
Color = OxyColor.FromArgb(120, 255, 0, 0),
StrokeThickness = 1.0,
TrackerFormatString =
"{0}" + Environment.NewLine +
"{1}: {2:0.###}" + Environment.NewLine +
"{3}: {4:0.###}" + Environment.NewLine +
"Index: {Index:0.###}"
};
PlotModel.Series.Add(actSeries);
}
else
{
// Create series for actual isotope profile
var actSeries = new PeakPointSeries
{
Title = "Observed",
ItemsSource = observed,
Color = OxyColor.FromArgb(120, 255, 0, 0),
StrokeThickness = 3.0,
TrackerFormatString =
"{0}" + Environment.NewLine +
"{1}: {2:0.###}" + Environment.NewLine +
"{3}: {4:0.###}" + Environment.NewLine +
"Index: {Index:0.###}"
};
PlotModel.Series.Add(actSeries);
}
// Calculate min and max boundaries for plot
var min = theoretical.Min(p => p.X);
var max = theoretical.Max(p => p.X);
min -= (max - min) / 3;
var absMin = Math.Max(0, min - 10);
max += (max - min) / 3;
var absMax = max + 10;
xaxis.Minimum = min;
xaxis.AbsoluteMinimum = absMin;
xaxis.Maximum = max;
xaxis.AbsoluteMaximum = absMax;
xaxis.Zoom(min, max);
PlotModel.IsLegendVisible = true;
PlotModel.InvalidatePlot(true);
PlotModel.AdjustForZoom();
}
/// <summary>
/// Build spectrum plot model.
/// </summary>
/// <param name="peakDataPoints">Ion peaks to highlight and annotate on spectrum plot.</param>
private void UpdatePlotModel(IList <PeakDataPoint>[] peakDataPoints)
{
if (this.Spectrum == null)
{
return;
}
this.errorMapViewModel.SetData(this.FragmentationSequenceViewModel.FragmentationSequence.Sequence, peakDataPoints);
this.PlotModel.Series.Clear();
this.PlotModel.Annotations.Clear();
this.currentSpectrum = this.GetSpectrum();
this.peakDataPoints = peakDataPoints;
var spectrumPeaks = currentSpectrum.Peaks.Select(peak => new PeakDataPoint(peak.Mz, peak.Intensity, 0.0, 0.0, string.Empty));
var spectrumSeries = new PeakPointSeries
{
ItemsSource = spectrumPeaks,
Color = OxyColors.Black,
StrokeThickness = 0.5,
TrackerFormatString =
"{0}" + Environment.NewLine +
"{1}: {2:0.###}" + Environment.NewLine +
"{3}: {4:0.##E0}"
};
if (this.ShowUnexplainedPeaks)
{
this.PlotModel.Series.Add(spectrumSeries);
}
if (this.autoZoomXAxis && this.spectrumDirty)
{
// zoom spectrum if this plot is supposed to be auto zoomed, and only if spectrum has changed
var peaks = currentSpectrum.Peaks;
var ms2MaxMz = 1.0; // plot maximum needs to be bigger than 0
if (peaks.Length > 0)
{
ms2MaxMz = peaks.Max().Mz * 1.1;
}
this.XAxis.AbsoluteMinimum = 0;
this.XAxis.AbsoluteMaximum = ms2MaxMz;
this.XAxis.Zoom(0, ms2MaxMz);
this.spectrumDirty = false;
}
var maxCharge = peakDataPoints.Length > 0 ? this.ions.Max(x => x.IonType.Charge) : 2;
maxCharge = Math.Max(maxCharge, 2);
var colors = new IonColorDictionary(maxCharge);
foreach (var points in peakDataPoints)
{
if (points.Count == 0 || points[0].Error.Equals(double.NaN))
{
continue;
}
var firstPoint = points[0];
var color = firstPoint.IonType != null?colors.GetColor(firstPoint.IonType.BaseIonType, firstPoint.IonType.Charge)
: colors.GetColor(firstPoint.Index);
var ionSeries = new PeakPointSeries
{
Color = color,
StrokeThickness = 1.5,
ItemsSource = points,
Title = points[0].Title,
TrackerFormatString =
"{0}" + Environment.NewLine +
"{1}: {2:0.###}" + Environment.NewLine +
"{3}: {4:0.##E0}" + Environment.NewLine +
"Error: {Error:G4}ppm" + Environment.NewLine +
"Correlation: {Correlation:0.###}"
};
// Create ion name annotation
var annotationName = points[0].Title.Contains("Precursor")
? string.Format("{0}\n{1,12:F3}",
points[0].Title,
points[0].X)
: points[0].Title;
var annotation = new TextAnnotation
{
Text = annotationName,
TextColor = color,
FontWeight = FontWeights.Bold,
Layer = AnnotationLayer.AboveSeries,
FontSize = 12,
Background = OxyColors.White,
Padding = new OxyThickness(0.1),
TextPosition = new DataPoint(points[0].X, points[0].Y),
TextHorizontalAlignment = HorizontalAlignment.Center,
StrokeThickness = 0
};
this.PlotModel.Series.Add(ionSeries);
this.PlotModel.Annotations.Add(annotation);
}
this.PlotModel.Title = this.Title;
this.PlotModel.InvalidatePlot(true);
this.PlotModel.AdjustForZoom();
}
private PlotModel GetPlotModel(PrSm id)
{
var lcms = id.LcMs;
var fragSequence = id.GetFragmentationSequence();
var msLevel = lcms.GetMsLevel(id.Scan);
var fragments = msLevel == 2 ?
fragSequence.GetFragmentLabels(ionTypes.Where(ionType => ionType.Charge <= id.Charge).ToList()) :
fragSequence.GetChargePrecursorLabels();
var spectrum = lcms.GetSpectrum(id.Scan, true);
// Set up plot
var plotModel = new PlotModel
{
Title = msLevel == 2 ? string.Format("MS/MS Scan {0}", id.Scan) :
string.Format("MS Scan {0}", id.Scan),
IsLegendVisible = false,
};
// Add axes
var xaxis = new LinearAxis {
Title = "M/Z", Position = AxisPosition.Bottom
};
var yaxis = new LinearAxis {
Title = "Intensity", Position = AxisPosition.Left, Minimum = 0
};
plotModel.Axes.Add(xaxis);
plotModel.Axes.Add(yaxis);
// Add spectrum peaks
var spectrumPeaks = spectrum.Peaks.Select(peak => new PeakDataPoint(peak.Mz, peak.Intensity, 0.0, 0.0, string.Empty));
var spectrumStemSeries = new StemSeries
{
ItemsSource = spectrumPeaks,
Color = OxyColors.Black,
StrokeThickness = 0.5,
};
plotModel.Series.Add(spectrumStemSeries);
// Add ion highlights
var colors = new IonColorDictionary(id.Charge);
foreach (var fragment in fragments)
{
var points = fragment.GetPeaks(spectrum, false, false);
if (points.Count == 0 || points[0].Error.Equals(double.NaN))
{
continue;
}
var firstPoint = points[0];
var color = firstPoint.IonType != null?colors.GetColor(firstPoint.IonType.BaseIonType, firstPoint.IonType.Charge)
: colors.GetColor(firstPoint.Index);
var ionSeries = new PeakPointSeries
{
Color = color,
StrokeThickness = 1.5,
ItemsSource = points,
Title = points[0].Title,
};
// Create ion name annotation
var annotation = new TextAnnotation
{
Text = points[0].Title,
TextColor = color,
FontWeight = FontWeights.Bold,
Layer = AnnotationLayer.AboveSeries,
FontSize = 12,
Background = OxyColors.White,
Padding = new OxyThickness(0.1),
TextPosition = new DataPoint(points[0].X, points[0].Y),
StrokeThickness = 0
};
plotModel.Series.Add(ionSeries);
plotModel.Annotations.Add(annotation);
}
return(plotModel);
}
