public void DisplaySpectrumMatch(PlotView plotView, Canvas canvas, PsmFromTsv psm, ParentChildScanPlotsView parentChildScanPlotsView, out List <string> errors)
{
errors = null;
// clear old parent/child scans
parentChildScanPlotsView.Plots.Clear();
CurrentlyDisplayedPlots.Clear();
// get the scan
if (!MsDataFiles.TryGetValue(psm.FileNameWithoutExtension, out DynamicDataConnection spectraFile))
{
errors = new List <string>();
errors.Add("The spectra file could not be found for this PSM: " + psm.FileNameWithoutExtension);
return;
}
MsDataScan scan = spectraFile.GetOneBasedScanFromDynamicConnection(psm.Ms2ScanNumber);
LibrarySpectrum librarySpectrum = null;
// plot the annotated spectrum match
PeptideSpectrumMatchPlot plot;
//if not crosslinked
if (psm.BetaPeptideBaseSequence == null)
{
// get the library spectrum if relevant
if (SpectralLibrary != null)
{
SpectralLibrary.TryGetSpectrum(psm.FullSequence, psm.PrecursorCharge, out var librarySpectrum1);
librarySpectrum = librarySpectrum1;
}
plot = new PeptideSpectrumMatchPlot(plotView, canvas, psm, scan, psm.MatchedIons, librarySpectrum: librarySpectrum);
}
else //crosslinked
{
plot = new CrosslinkSpectrumMatchPlot(plotView, canvas, psm, scan);
}
CurrentlyDisplayedPlots.Add(plot);
// plot parent/child scans
if (psm.ChildScanMatchedIons != null)
{
// draw parent scan
string parentAnnotation = "Scan: " + scan.OneBasedScanNumber
+ " Dissociation Type: " + scan.DissociationType
+ " MsOrder: " + scan.MsnOrder
+ " Selected Mz: " + scan.SelectedIonMZ.Value.ToString("0.##")
+ " Retention Time: " + scan.RetentionTime.ToString("0.##");
var parentPlotView = new PlotView(); // placeholder
var parentCanvas = new Canvas();
var item = new ParentChildScanPlotTemplate()
{
Plot = new PeptideSpectrumMatchPlot(parentPlotView, parentCanvas, psm, scan, psm.MatchedIons),
SpectrumLabel = parentAnnotation,
TheCanvas = parentCanvas
};
parentChildScanPlotsView.Plots.Add(item);
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
parentPlotView.Model = null;
// draw child scans
HashSet <int> scansDrawn = new HashSet <int>();
var allChildScanMatchedIons = psm.ChildScanMatchedIons;
if (psm.BetaPeptideChildScanMatchedIons != null)
{
allChildScanMatchedIons = allChildScanMatchedIons.Concat(psm.BetaPeptideChildScanMatchedIons)
.GroupBy(p => p.Key)
.ToDictionary(p => p.Key, q => q.SelectMany(p => p.Value).ToList());
}
foreach (var childScanMatchedIons in allChildScanMatchedIons)
{
int childScanNumber = childScanMatchedIons.Key;
if (scansDrawn.Contains(childScanNumber))
{
continue;
}
scansDrawn.Add(childScanNumber);
List <MatchedFragmentIon> matchedIons = childScanMatchedIons.Value;
MsDataScan childScan = spectraFile.GetOneBasedScanFromDynamicConnection(childScanNumber);
string childAnnotation = "Scan: " + childScan.OneBasedScanNumber
+ " Dissociation Type: " + childScan.DissociationType
+ " MsOrder: " + childScan.MsnOrder
+ " Selected Mz: " + childScan.SelectedIonMZ.Value.ToString("0.##")
+ " RetentionTime: " + childScan.RetentionTime.ToString("0.##");
Canvas childCanvas = new Canvas();
PlotView childPlotView = new PlotView(); // placeholder
// make the plot
var childPlot = new PeptideSpectrumMatchPlot(childPlotView, childCanvas, psm, childScan, matchedIons, annotateProperties: false);
childPlot.Model.Title = null;
childPlot.Model.Subtitle = null;
item = new ParentChildScanPlotTemplate()
{
Plot = childPlot, SpectrumLabel = childAnnotation, TheCanvas = childCanvas
};
// remove model from placeholder (the model can only be referenced by 1 plotview at a time)
childPlotView.Model = null;
parentChildScanPlotsView.Plots.Add(item);
CurrentlyDisplayedPlots.Add(childPlot);
}
}
}
//draw the sequence coverage map: write out the sequence, overlay modifications, and display matched fragments
public void DrawSequenceCoverageMap(PsmFromTsv psm, Canvas sequenceText, Canvas map)
{
map.Children.Clear();
sequenceText.Children.Clear();
int spacing = 20;
const int textHeight = 140;
const int heightIncrement = 5;
const int xShift = 10;
int peptideLength = psm.BaseSeq.Length;
//intensity arrays for each ion type
double[] nIntensityArray = new double[peptideLength - 1];
double[] cIntensityArray = new double[peptideLength - 1];
double[] internalIntensityArray = new double[peptideLength - 1];
//colors for annotation
Color nColor = Colors.Blue;
Color cColor = Colors.Red;
Color internalColor = Colors.Purple;
//draw sequence text
for (int r = 0; r < psm.BaseSeq.Length; r++)
{
TextDrawing(sequenceText, new Point(r * spacing + xShift, textHeight - 30), (r + 1).ToString(), Brushes.Black, 8);
TextDrawing(sequenceText, new Point(r * spacing + xShift, textHeight - 15), (psm.BaseSeq.Length - r).ToString(), Brushes.Black, 8);
TextDrawing(sequenceText, new Point(r * spacing + xShift, textHeight), psm.BaseSeq[r].ToString(), Brushes.Black, 16);
}
//create circles for mods, if needed and able
if (!psm.FullSequence.Contains("|")) //can't draw mods if not localized/identified
{
PeptideSpectrumMatchPlot.AnnotateModifications(psm, sequenceText, psm.FullSequence, textHeight - 4, spacing, xShift + 5);
}
//draw lines for each matched fragment
List <bool[]> index = new List <bool[]>();
//N-terminal
List <MatchedFragmentIon> nTermFragments = psm.MatchedIons.Where(x => x.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.N).ToList();
//C-terminal in reverse order
List <MatchedFragmentIon> cTermFragments = psm.MatchedIons.Where(x => x.NeutralTheoreticalProduct.Terminus == FragmentationTerminus.C).OrderByDescending(x => x.NeutralTheoreticalProduct.FragmentNumber).ToList();
//add internal fragments
List <MatchedFragmentIon> internalFragments = psm.MatchedIons.Where(x => x.NeutralTheoreticalProduct.SecondaryProductType != null).OrderBy(x => x.NeutralTheoreticalProduct.FragmentNumber).ToList();
//indexes to navigate terminal ions
int n = 0;
int c = 0;
int heightForThisFragment = 70; //location to draw a fragment
//line up terminal fragments so that complementary ions are paired on the same line
while (n < nTermFragments.Count && c < cTermFragments.Count)
{
MatchedFragmentIon nProduct = nTermFragments[n];
MatchedFragmentIon cProduct = cTermFragments[c];
int expectedComplementary = peptideLength - nProduct.NeutralTheoreticalProduct.FragmentNumber;
//if complementary pair
if (cProduct.NeutralTheoreticalProduct.FragmentNumber == expectedComplementary)
{
//plot sequences
DrawHorizontalLine(0, nProduct.NeutralTheoreticalProduct.FragmentNumber, map, heightForThisFragment, nColor, spacing);
DrawHorizontalLine(peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber, peptideLength, map, heightForThisFragment, cColor, spacing);
//record intensities
nIntensityArray[nProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += nProduct.Intensity;
cIntensityArray[peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += cProduct.Intensity;
//increment indexes
n++;
c++;
}
//if n-terminal ion is present without complementary
else if (cProduct.NeutralTheoreticalProduct.FragmentNumber < expectedComplementary)
{
DrawHorizontalLine(0, nProduct.NeutralTheoreticalProduct.FragmentNumber, map, heightForThisFragment, nColor, spacing);
nIntensityArray[nProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += nProduct.Intensity;
n++;
}
//if c-terminal ion is present without complementary
else
{
DrawHorizontalLine(peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber, peptideLength, map, heightForThisFragment, cColor, spacing);
cIntensityArray[peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += cProduct.Intensity;
c++;
}
heightForThisFragment += heightIncrement;
}
//wrap up leftover fragments without complementary pairs
for (; n < nTermFragments.Count; n++)
{
MatchedFragmentIon nProduct = nTermFragments[n];
DrawHorizontalLine(0, nProduct.NeutralTheoreticalProduct.FragmentNumber, map, heightForThisFragment, nColor, spacing);
nIntensityArray[nProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += nProduct.Intensity;
heightForThisFragment += heightIncrement;
}
for (; c < cTermFragments.Count; c++)
{
MatchedFragmentIon cProduct = cTermFragments[c];
DrawHorizontalLine(peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber, peptideLength, map, heightForThisFragment, cColor, spacing);
cIntensityArray[peptideLength - cProduct.NeutralTheoreticalProduct.FragmentNumber - 1] += cProduct.Intensity;
heightForThisFragment += heightIncrement;
}
//internal fragments
foreach (MatchedFragmentIon fragment in internalFragments)
{
DrawHorizontalLine(fragment.NeutralTheoreticalProduct.FragmentNumber, fragment.NeutralTheoreticalProduct.SecondaryFragmentNumber, map, heightForThisFragment, internalColor, spacing);
internalIntensityArray[fragment.NeutralTheoreticalProduct.FragmentNumber - 1] += fragment.Intensity;
internalIntensityArray[fragment.NeutralTheoreticalProduct.SecondaryFragmentNumber - 1] += fragment.Intensity;
heightForThisFragment += heightIncrement;
}
map.Height = heightForThisFragment + 100;
map.Width = spacing * psm.BaseSeq.Length + 100;
sequenceText.Width = spacing * psm.BaseSeq.Length + 100;
////PLOT INTENSITY HISTOGRAM////
double[] intensityArray = new double[peptideLength - 1];
for (int i = 0; i < intensityArray.Length; i++)
{
intensityArray[i] = nIntensityArray[i] + cIntensityArray[i] + internalIntensityArray[i];
}
double maxIntensity = intensityArray.Max();
//foreach cleavage site
for (int i = 0; i < intensityArray.Length; i++)
{
//if anything
if (intensityArray[i] > 0)
{
int x = (i + 1) * spacing + 7;
//n-terminal
int nY = 100 - (int)Math.Round(nIntensityArray[i] * 100 / maxIntensity, 0);
if (nY != 100)
{
DrawVerticalLine(104, nY + 4, sequenceText, (i + 1) * spacing + 5, nColor);
}
//c-terminal
int cY = nY - (int)Math.Round(cIntensityArray[i] * 100 / maxIntensity, 0);
if (nY != cY)
{
DrawVerticalLine(nY + 2, cY + 2, sequenceText, (i + 1) * spacing + 5, cColor);
}
//internal
int iY = cY - (int)Math.Round(internalIntensityArray[i] * 100 / maxIntensity, 0);
if (cY != iY)
{
DrawVerticalLine(cY, iY, sequenceText, (i + 1) * spacing + 5, internalColor);
}
}
}
}
