/// <summary>
/// Builds the isotopic profile plot based on the selected isotope ratios.
/// </summary>
private void BuildIsotopicProfilePlot()
{
if (this.Mass.Equals(0.0))
{ // Mass has not been set
return;
}
// Set up the concentration tuner if any of the proportions changed.
var predictor = new IsoProfilePredictor(
this.IsotopeProportions["C"].GetProportions(),
this.IsotopeProportions["H"].GetProportions(),
this.IsotopeProportions["N"].GetProportions(),
this.IsotopeProportions["O"].GetProportions(),
this.IsotopeProportions["S"].GetProportions(),
this.RelativeIntensityThreshold
);
var averagine = new Averagine();
var theoreticalPeaks = averagine.GetTheoreticalIsotopeProfileInst(
this.Mass,
this.Charge,
this.RelativeIntensityThreshold,
predictor);
//var actualPeaks = isotopicConcentrationTuner.AlignObservedPeaks(
// this.ObservedPeaks.Select(peakDataPoint => new Peak(peakDataPoint.X, peakDataPoint.Y)).ToList(),
// theoreticalPeaks);
this.IsotopicEnvelopePlotViewModel.BuildPlot(
theoreticalPeaks,
this.ObservedPeaks.Select(pd => new Peak(pd.Item.X, pd.Item.Y)).ToList(),
this.IsProfile);
}
public void TestFitMinusOneScore(int precursor, string adduct, string commonName, string id, string rawFilePath)
{
var lipid = new Lipid()
{
AdductFull = adduct, CommonName = commonName
};
var lipidTarget = lipid.CreateLipidTarget();
var composition = lipidTarget.Composition;
var compMinus1 = new Composition(composition.C, composition.H - 1, composition.N, composition.O, composition.S, composition.P); //Subtract one hydrogen to make this a minus1 fit score
var lcmsRun = PbfLcMsRun.GetLcMsRun(rawFilePath);
var spectrum = lcmsRun.GetSpectrum(precursor);
var relativeIntensityThreshold = 0.1;
var tolerance = new Tolerance(30, ToleranceUnit.Ppm);
//Get the values to use to calculate pearson correlation
var observedPeaks = LipidUtil.GetAllIsotopePeaks(spectrum, compMinus1, tolerance,
relativeIntensityThreshold);
if (observedPeaks == null)
{
Console.WriteLine("Observed peaks is null for scan " + id);
}
var isotopomerEnvelope = IsoProfilePredictor.GetIsotopomerEnvelop(
compMinus1.C,
compMinus1.H,
compMinus1.N,
compMinus1.O,
compMinus1.S);
var observedIntensities = new double[observedPeaks.Length];
for (var i = 0; i < observedPeaks.Length; i++)
{
var observedPeak = observedPeaks[i];
observedIntensities[i] = observedPeak != null ? (float)observedPeak.Intensity : 0.0;
}
Console.WriteLine("The theoretical y values are: ");
foreach (var value in isotopomerEnvelope.Envolope)
{
Console.WriteLine(value + ", ");
}
Console.WriteLine("The observed peak intensity x values are: ");
foreach (var value in observedIntensities)
{
Console.WriteLine(value + ", ");
}
}
/// <summary>
/// Get the theoretical isotopic distribution for the given composition.
/// </summary>
/// <param name="composition">The composition to calculate the theoretical isotopic profile.</param>
/// <param name="relativeIntensityThreshold">The least abundant peak to consider as a percentage of the most abundant peak.</param>
/// <returns>The theoretical isotopic distribution.</returns>
private double[] GetTheoreticalIntensities(Composition composition, double relativeIntensityThreshold = 0.1)
{
var isotopomerEnvelope = IsoProfilePredictor.GetIsotopomerEnvelop(
composition.C,
composition.H,
composition.N,
composition.O,
composition.S);
return(isotopomerEnvelope.Envolope.TakeWhile(isotope => !(isotope < relativeIntensityThreshold)).ToArray());
}
/// <summary>
/// Gets the theoretical isotope profile calculated using Averagine with the provided
/// isotope proportions.
/// </summary>
/// <param name="proportions">The proportions of each isotope.</param>
/// <returns>The theoretical isotope profile peaks.</returns>
public List <Peak> GetTheoreticalIsotopeProfile(double[] proportions)
{
// Get IsoProfilePredictor with updated proportions
var isoProfilePredictor = new IsoProfilePredictor(
Element.Code == "C" ? proportions : IsoProfilePredictor.DefaultProbC,
Element.Code == "H" ? proportions : IsoProfilePredictor.DefaultProbH,
Element.Code == "N" ? proportions : IsoProfilePredictor.DefaultProbN,
Element.Code == "O" ? proportions : IsoProfilePredictor.DefaultProbO,
Element.Code == "S" ? proportions : IsoProfilePredictor.DefaultProbS
);
var averagine = new Averagine();
return(averagine.GetTheoreticalIsotopeProfileInst(
Mass,
Charge,
RelativeIntensityThreshold,
isoProfilePredictor));
}
