public MainWindow()
{
InitializeComponent();
dataGridPeptideFiles.DataContext = DataFilesObservableCollection;
dataGridDatabaseFiles.DataContext = DatabasesObservableCollection;
DisplayedSamplesDataGrid.DataContext = FilesToDisplayObservableCollection;
HiddenSamplesDataGrid.DataContext = FilesToHideObservableCollection;
DisplayAnalyzedFilesDataGrid.DataContext = DataFilesObservableCollection;
HalfLifeHistogramPlot.Configure(enableScrollWheelZoom: false);
PrecisionPlot.Configure(enableScrollWheelZoom: false);
HalfLifeComparisonPlot.Configure(enableScrollWheelZoom: false);
RatioComparisonPlot.Configure(enableScrollWheelZoom: false);
peptideRadioButton.IsChecked = true;
proteinSpecificRadioButton.IsChecked = DisplayProteinInSpecificTable;
DisplayPeptidesView = CollectionViewSource.GetDefaultView(PeptidesToDisplay);
DisplayPeptidesDataGrid.DataContext = DisplayPeptidesView;
Loaders.LoadElements();
PopulateChoices();
}
private void PlotHalfLifeHistogram(List <PeptideTurnoverObject> peptidesToPlot)
{
HalfLifeHistogramPlot.plt.Clear();
HalfLifeHistogramPlot.plt.GetPlottables().Clear();
double[] halflives = peptidesToPlot.Select(x => Math.Log(2, Math.E) / x.Kbi).ToArray();
Histogram histogram = new Histogram(halflives, 0, 100, 0.5);
double barWidth = histogram.binSize * 1.2; // slightly over-side to reduce anti-alias rendering artifacts
HalfLifeHistogramPlot.plt.Axis(0, 50, 0, histogram.counts.Max() * 1.1);
HalfLifeHistogramPlot.plt.PlotBar(histogram.bins, histogram.counts, barWidth: barWidth, outlineWidth: 0);
if (peptideRadioButton.IsChecked.Value)
{
HalfLifeHistogramPlot.plt.YLabel("Frequency (# Peptides)");
}
else
{
HalfLifeHistogramPlot.plt.YLabel("Frequency (# Proteins)");
HalfLifeHistogramPlot.plt.YLabel("Number of Proteins", fontSize: 24);
}
HalfLifeHistogramPlot.plt.XLabel("Half-life (Days)", fontSize: 24);
HalfLifeHistogramPlot.plt.Axis(0, 50, 0, histogram.counts.Max() * 1.1);
HalfLifeComparisonPlot.Render(); HalfLifeComparisonPlot.Render();
}
private void PlotPeptideData(List <PeptideTurnoverObject> peptidesToPlot)
{
RatioComparisonPlot.plt.Clear();
RatioComparisonPlot.plt.Legend(false);
HalfLifeComparisonPlot.plt.GetPlottables().Clear();
//if (PlotAminoAcidPoolCheckBox.IsChecked.Value)
//{
// foreach (string file in FilesToDisplayObservableCollection)
// {
// PlotFit(PoolParameterDictionary[file], Path.GetFileNameWithoutExtension(file)+" Free Amino Acids");
// }
//}
double minError = double.PositiveInfinity;
double maxError = double.NegativeInfinity;
double minHalfLife = double.PositiveInfinity;
double maxHalfLife = double.NegativeInfinity;
int debug = 0;
foreach (PeptideTurnoverObject peptide in peptidesToPlot)
{
debug++;
//get the title
int fontSize = Math.Max(Math.Min(24, 100 / (int)Math.Round(Math.Sqrt(peptide.DisplayPeptideSequence.Length))), 12);
RatioComparisonPlot.plt.Title(peptide.DisplayPeptideSequence, fontSize: fontSize);
string protein = peptide.DisplayProteinOrProteoform;
string filepath = peptide.FileName;
string filename = Path.GetFileNameWithoutExtension(filepath);
//plot actual data
RatioComparisonPlot.plt.PlotScatter(peptide.Timepoints, peptide.RelativeFractions, markerSize: 4, lineWidth: 0, label: filename + " Observed Ratios");
//Plot protein info
List <PeptideTurnoverObject> peptidesSharingProteinAndFile = PeptidesToDisplay.Where(x => x.DisplayProteinOrProteoform.Equals(protein) && x.FileName.Equals(filepath)).ToList();
double[] errors = peptidesSharingProteinAndFile.Select(x => x.Error).ToArray();
double[] halfLives = peptidesSharingProteinAndFile.Select(x => Math.Log(2, Math.E) / x.Kbi).ToArray();
double[] negativeErrors = peptidesSharingProteinAndFile.Select(x => (Math.Log(2, Math.E) / x.Kbi) - (Math.Log(2, Math.E) / x.HighKbi)).ToArray();
double[] positiveErrors = peptidesSharingProteinAndFile.Select(x => (Math.Log(2, Math.E) / x.LowKbi) - (Math.Log(2, Math.E) / x.Kbi)).ToArray();
HalfLifeComparisonPlot.plt.Title(protein, fontSize: 24);
HalfLifeComparisonPlot.plt.Layout(titleHeight: 20, xLabelHeight: 40, y2LabelWidth: 20);
HalfLifeComparisonPlot.plt.YLabel("Half-life (Days)", fontSize: 20);
HalfLifeComparisonPlot.plt.XLabel("Error (MSE)", fontSize: 20);
HalfLifeComparisonPlot.plt.Ticks(fontSize: 18);
double errorDiff = errors.Max() - errors.Min();
if (errorDiff == 0)
{
errorDiff = 0.01;
}
double halflifeDiff = halfLives.Max() - halfLives.Min();
if (halflifeDiff == 0)
{
halflifeDiff = 0.01;
}
var scatter = HalfLifeComparisonPlot.plt.PlotScatter(errors, halfLives, lineWidth: 0, label: filename + " peptides", color: Color.SteelBlue);//debug == 1 ? Color.DodgerBlue : Color.Red);
//plot the single point of the selected peptie separately (overlay) so that we know which one it is
var point = HalfLifeComparisonPlot.plt.PlotPoint(peptide.Error, Math.Log(2, Math.E) / peptide.Kbi, color: Color.Black);
//plot errors
HalfLifeComparisonPlot.plt.PlotErrorBars(errors, halfLives, null, null, positiveErrors, negativeErrors, scatter.color);
HalfLifeComparisonPlot.plt.PlotErrorBars(new double[] { peptide.Error }, new double[] { Math.Log(2, Math.E) / peptide.Kbi },
null, null, new double[] { (Math.Log(2, Math.E) / peptide.LowKbi) - (Math.Log(2, Math.E) / peptide.Kbi) },
new double[] { (Math.Log(2, Math.E) / peptide.Kbi) - (Math.Log(2, Math.E) / peptide.HighKbi) }, color: point.color);
minError = Math.Min(minError, errors.Min() - errorDiff * 0.2);
maxError = Math.Max(maxError, errors.Max() + errorDiff * 0.2);
minHalfLife = Math.Min(minHalfLife, halfLives.Min() - negativeErrors.Max() - halflifeDiff * 0.2);
maxHalfLife = Math.Max(maxHalfLife, halfLives.Max() + positiveErrors.Max() + halflifeDiff * 0.2);
double ySpacingFactor = (maxHalfLife - minHalfLife) * 0.2;
HalfLifeComparisonPlot.plt.Axis(minError, maxError, minHalfLife - ySpacingFactor, maxHalfLife + ySpacingFactor);
HalfLifeComparisonPlot.plt.Axis();
PeptideTurnoverObject currentProtein = DisplayProteinInSpecificTable ?
AnalyzedProteins.Where(x => x.Protein.Equals(protein) && x.FileName.Equals(filepath)).FirstOrDefault() :
AnalyzedProteoforms.Where(x => x.Proteoform.Equals(protein) && x.FileName.Equals(filepath)).FirstOrDefault();
if (currentProtein == null)
{
MessageBox.Show("Unable to find the protein for this peptide. There may be an issue with the loaded file.");
return;
}
//plot the fit
if (PlotBestFitCheckBox.IsChecked.Value)
{
//peptide level
PlotFit(PoolParameterDictionary[filepath], filename + " Fit (" + (Math.Log(2, Math.E) / peptide.Kbi).ToString("F1") + " d)", peptide.Kbi);
//protein level
double halfLife = Math.Log(2, Math.E) / currentProtein.Kbi;
HalfLifeComparisonPlot.plt.PlotHLine(halfLife, label: filename + " Half-life (" + halfLife.ToString("F1") + ")", color: Color.OrangeRed);//debug == 1 ? Color.DodgerBlue : Color.Red);
}
//plt the confidence intervals
if (PlotCICheckBox.IsChecked.Value)
{
//peptide level
PlotFit(PoolParameterDictionary[filepath], filename + " Upper CI (" + (Math.Log(2, Math.E) / peptide.LowKbi).ToString("F1") + " d)", peptide.LowKbi);
PlotFit(PoolParameterDictionary[filepath], filename + " Lower CI (" + (Math.Log(2, Math.E) / peptide.HighKbi).ToString("F1") + " d)", peptide.HighKbi);
//protein level
double upperHL = Math.Log(2, Math.E) / currentProtein.LowKbi;
double lowerHL = Math.Log(2, Math.E) / currentProtein.HighKbi;
HalfLifeComparisonPlot.plt.PlotHLine(upperHL, label: filename + " Upper CI (" + upperHL.ToString("F1") + ")", color: Color.Green);
HalfLifeComparisonPlot.plt.PlotHLine(lowerHL, label: filename + " Lower CI (" + lowerHL.ToString("F1") + ")", color: Color.Red);
}
}
if (PlotAminoAcidPoolCheckBox.IsChecked.Value)
{
foreach (string file in FilesToDisplayObservableCollection)
{
PlotFit(PoolParameterDictionary[file], Path.GetFileNameWithoutExtension(file) + " Free Amino Acids");
}
}
if (DisplayLegendCheckBox.IsChecked.Value)
{
HalfLifeComparisonPlot.plt.Legend();
}
else
{
HalfLifeComparisonPlot.plt.Legend(false);
}
HalfLifeComparisonPlot.Render();
}