public QuantificationResult GetQuantification()
{
var quantifier = PeptideQuantifier.GetPeptideQuantifier(SrmDocument.Settings, Peptide.Protein.DocNode, Peptide.DocNode);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(quantifier, SrmDocument.Settings);
return(curveFitter.GetQuantificationResult(ResultFile.Replicate.ReplicateIndex));
}
private string GetFormTitle(CalibrationCurveFitter curveFitter)
{
string title = TextUtil.SpaceSeparate(_originalFormTitle + ':', curveFitter.PeptideQuantifier.PeptideDocNode.ModifiedSequenceDisplay);
if (curveFitter.SingleBatchReplicateIndex.HasValue)
{
var chromatogramSet = _skylineWindow.Document.Settings.MeasuredResults.Chromatograms[
curveFitter.SingleBatchReplicateIndex.Value];
if (string.IsNullOrEmpty(chromatogramSet.BatchName))
{
title = TextUtil.SpaceSeparate(title, string.Format(QuantificationStrings.CalibrationForm_GetFormTitle__Replicate___0__, chromatogramSet.Name));
}
else
{
title = TextUtil.SpaceSeparate(title, string.Format(QuantificationStrings.CalibrationForm_GetFormTitle__Batch___0__, chromatogramSet.BatchName));
}
}
else
{
if (_skylineWindow.Document.Settings.HasResults && _skylineWindow.Document.Settings.MeasuredResults
.Chromatograms.Select(c => c.BatchName).Distinct().Count() > 1)
{
title = TextUtil.SpaceSeparate(title, QuantificationStrings.CalibrationForm_GetFormTitle__All_Replicates_);
}
}
return(title);
}
private void zedGraphControl_ContextMenuBuilder(ZedGraphControl sender, ContextMenuStrip menuStrip, Point mousePt, ZedGraphControl.ContextMenuObjectState objState)
{
var calibrationCurveOptions = Settings.Default.CalibrationCurveOptions;
singleBatchContextMenuItem.Checked = calibrationCurveOptions.SingleBatch;
if (IsEnableIsotopologResponseCurve())
{
singleBatchContextMenuItem.Visible = true;
showSampleTypesContextMenuItem.Visible = false;
}
else
{
singleBatchContextMenuItem.Visible = CalibrationCurveFitter.AnyBatchNames(_skylineWindow.Document.Settings);
showSampleTypesContextMenuItem.Visible = true;
}
var replicateIndexFromPoint = ReplicateIndexFromPoint(mousePt);
if (replicateIndexFromPoint.HasValue && null == replicateIndexFromPoint.Value.LabelType)
{
ToolStripMenuItem excludeStandardMenuItem
= MakeExcludeStandardMenuItem(replicateIndexFromPoint.Value.ReplicateIndex);
if (excludeStandardMenuItem != null)
{
menuStrip.Items.Clear();
menuStrip.Items.Add(excludeStandardMenuItem);
return;
}
}
showSampleTypesContextMenuItem.DropDownItems.Clear();
foreach (var sampleType in SampleType.ListSampleTypes())
{
showSampleTypesContextMenuItem.DropDownItems.Add(MakeShowSampleTypeMenuItem(sampleType));
}
logXContextMenuItem.Checked = Options.LogXAxis;
logYAxisContextMenuItem.Checked = Options.LogYAxis;
showLegendContextMenuItem.Checked = Options.ShowLegend;
showSelectionContextMenuItem.Checked = Options.ShowSelection;
showFiguresOfMeritContextMenuItem.Checked = Options.ShowFiguresOfMerit;
ZedGraphHelper.BuildContextMenu(sender, menuStrip, true);
if (!menuStrip.Items.Contains(logXContextMenuItem))
{
int index = 0;
menuStrip.Items.Insert(index++, logXContextMenuItem);
menuStrip.Items.Insert(index++, logYAxisContextMenuItem);
menuStrip.Items.Insert(index++, showSampleTypesContextMenuItem);
menuStrip.Items.Insert(index++, singleBatchContextMenuItem);
menuStrip.Items.Insert(index++, showLegendContextMenuItem);
menuStrip.Items.Insert(index++, showSelectionContextMenuItem);
menuStrip.Items.Insert(index++, showFiguresOfMeritContextMenuItem);
menuStrip.Items.Insert(index++, new ToolStripSeparator());
}
}
private CalibrationCurveFitter GetCalibrationCurveFitter()
{
if (string.IsNullOrEmpty(ResultFile.Replicate.BatchName) && !Peptide.DocNode.HasPrecursorConcentrations)
{
return(Peptide.GetCalibrationCurveFitter());
}
var calibrationCurveFitter =
new CalibrationCurveFitter(Peptide.GetPeptideQuantifier(), SrmDocument.Settings);
calibrationCurveFitter.SingleBatchReplicateIndex = ResultFile.Replicate.ReplicateIndex;
return(calibrationCurveFitter);
}
public void TestSinglePointExternalCalibrationWithIsConcentration()
{
const double internalStandardConcentration = 80.0;
var srmDocument = LoadTestDocument();
srmDocument = ChangeStandardConcentrationCount(srmDocument, 1);
srmDocument = ChangeQuantificationSettings(srmDocument, QuantificationSettings.DEFAULT
.ChangeRegressionFit(RegressionFit.LINEAR_THROUGH_ZERO)
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy)));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = protein.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(internalStandardConcentration);
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(srmDocument.Settings, protein, peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, srmDocument.Settings);
Assert.AreEqual(CalibrationCurveFitter.ConcentrationRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy),
curveFitter.GetXAxisTitle());
Assert.AreEqual(CalibrationCurveFitter.PeakAreaRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy), curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = peptide.Results[iReplicate].First().LabelRatios.First().Ratio.Ratio;
double?actualY = curveFitter.GetYValue(iReplicate).Value;
Assert.IsNotNull(actualY);
Assert.AreEqual(expectedY, actualY.Value, epsilon, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.AreEqual(1, calibrationCurve.PointCount);
var expectedConcentration = expectedY * internalStandardConcentration / calibrationCurve.Slope.Value;
Assert.AreEqual(expectedConcentration / internalStandardConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
var chromatogramSet = chromatograms[iReplicate];
if (Equals(chromatogramSet.SampleType, SampleType.STANDARD) && chromatogramSet.AnalyteConcentration.HasValue)
{
// Since there was only one standard, the regression line goes exactly through this sample.
Assert.AreEqual(expectedConcentration, chromatogramSet.AnalyteConcentration.Value * peptide.ConcentrationMultiplier.GetValueOrDefault(1.0), epsilon);
}
}
}
public void TestDilutionFactor()
{
var baseDocument = LoadTestDocument();
baseDocument = ChangeQuantificationSettings(baseDocument,
QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy))
.ChangeRegressionFit(RegressionFit.LINEAR)
.ChangeUnits("ng/mL"));
var baseCurveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(baseDocument.Settings,
baseDocument.MoleculeGroups.First(), baseDocument.Molecules.First());
var baseCurve = baseCurveFitter.GetCalibrationCurve();
// Set the dilution factor of each external standard to 2.0, and each unknown to 3.0
var docWithDilutionFactor = baseDocument.ChangeMeasuredResults(
baseDocument.MeasuredResults.ChangeChromatograms(baseDocument.MeasuredResults.Chromatograms.Select(
chrom => Equals(chrom.SampleType, SampleType.STANDARD) ? chrom.ChangeDilutionFactor(2.0) :
chrom.ChangeDilutionFactor(3.0)).ToArray()));
var dilutionFactorCurveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(
docWithDilutionFactor.Settings, docWithDilutionFactor.MoleculeGroups.First(),
docWithDilutionFactor.Molecules.First());
var dilutionFactorCurve = dilutionFactorCurveFitter.GetCalibrationCurve();
Assert.AreEqual(2.0 * baseCurve.Slope, dilutionFactorCurve.Slope);
Assert.AreEqual(baseCurve.Intercept, dilutionFactorCurve.Intercept);
for (int replicateIndex = 0; replicateIndex < baseDocument.MeasuredResults.Chromatograms.Count; replicateIndex++)
{
var sampleType = baseDocument.MeasuredResults.Chromatograms[replicateIndex].SampleType;
var baseConcentration = baseCurveFitter.GetCalculatedConcentration(baseCurve, replicateIndex);
Assert.IsNotNull(baseConcentration);
var dilutionFactorConcentration =
dilutionFactorCurveFitter.GetCalculatedConcentration(dilutionFactorCurve, replicateIndex);
Assert.IsNotNull(dilutionFactorConcentration);
if (Equals(sampleType, SampleType.STANDARD))
{
Assert.AreEqual(baseConcentration.Value, dilutionFactorConcentration.Value, epsilon);
}
else
{
Assert.AreEqual(1.5 * baseConcentration.Value, dilutionFactorConcentration.Value, epsilon);
}
}
AssertEx.ValidatesAgainstSchema(docWithDilutionFactor);
}
public void TestMultipointExternalCalibrationWithoutNormalization()
{
var srmDocument = LoadTestDocument();
srmDocument = ChangeQuantificationSettings(srmDocument,
QuantificationSettings.DEFAULT
.ChangeNormalizationMethod(NormalizationMethod.NONE)
.ChangeRegressionFit(RegressionFit.LINEAR)
.ChangeUnits("ng/mL"));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = srmDocument.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(null);
CalibrationCurveFitter curveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(srmDocument.Settings, protein, peptide);
string expectedXAxis = CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, "ng/mL");
Assert.AreEqual(expectedXAxis, curveFitter.GetXAxisTitle());
string expectedYAxis = QuantificationStrings.CalibrationCurveFitter_GetYAxisTitle_Peak_Area;
Assert.AreEqual(expectedYAxis, curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
var lightPrecursor = peptide.TransitionGroups
.First(tg => IsotopeLabelType.light.Equals(tg.TransitionGroup.LabelType));
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = lightPrecursor.Results[iReplicate].First().Area.Value;
Assert.AreEqual(expectedY, curveFitter.GetYValue(iReplicate).Value, .01, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.IsNotNull(calibrationCurve.Slope);
Assert.IsNotNull(calibrationCurve.RSquared);
double expectedConcentration = calibrationCurve.GetX(expectedY).Value;
Assert.AreEqual(expectedConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
}
}
public void TestInternalCalibration()
{
const double internalStandardConcentration = 80.0;
var srmDocument = LoadTestDocument();
AssertEx.IsDocumentState(srmDocument, null, 1, 1, 2, 10);
srmDocument = ChangeStandardConcentrationCount(srmDocument, 0);
srmDocument = ChangeQuantificationSettings(srmDocument,
QuantificationSettings.DEFAULT
.ChangeRegressionFit(RegressionFit.NONE)
.ChangeNormalizationMethod(NormalizationMethod.GetNormalizationMethod(IsotopeLabelType.heavy))
.ChangeUnits("ng/mL"));
PeptideGroupDocNode protein = srmDocument.MoleculeGroups.First();
PeptideDocNode peptide = protein.Peptides.First();
peptide = peptide.ChangeInternalStandardConcentration(internalStandardConcentration);
CalibrationCurveFitter curveFitter = CalibrationCurveFitter.GetCalibrationCurveFitter(srmDocument.Settings, protein, peptide);
string expectedXAxis = CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, "ng/mL");
Assert.AreEqual(expectedXAxis, curveFitter.GetXAxisTitle());
string expectedYAxis = CalibrationCurveFitter.PeakAreaRatioText(IsotopeLabelType.light, IsotopeLabelType.heavy);
Assert.AreEqual(expectedYAxis, curveFitter.GetYAxisTitle());
var chromatograms = srmDocument.Settings.MeasuredResults.Chromatograms;
for (int iReplicate = 0; iReplicate < chromatograms.Count; iReplicate++)
{
string msg = string.Format("Replicate {0}", iReplicate);
var expectedY = peptide.Results[iReplicate].First().LabelRatios.First().Ratio.Ratio;
Assert.AreEqual(expectedY, curveFitter.GetYValue(iReplicate).Value, epsilon, msg);
var calibrationCurve = curveFitter.GetCalibrationCurve();
Assert.AreEqual(1 / internalStandardConcentration, calibrationCurve.Slope);
Assert.IsNull(calibrationCurve.RSquared);
Assert.AreEqual(expectedY * internalStandardConcentration,
curveFitter.GetCalculatedXValue(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
Assert.AreEqual(expectedY * internalStandardConcentration,
curveFitter.GetCalculatedConcentration(calibrationCurve, iReplicate).GetValueOrDefault(double.NaN), epsilon, msg);
}
}
protected override void DoTest()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification over Transition Settings", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 11);
// Peptide Quantitification Settings p. 11
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
PauseForScreenShot("Peptide Settings Quantification Tab", 12);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Specify analyte concentrations of external standards
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
var documentGridForm = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
for (int iRow = 0; iRow < concentrations.Length; iRow++)
{
// ReSharper disable AccessToModifiedClosure
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.Rows[iRow].Cells[colSampleType.Index].Value = SampleType.STANDARD;
});
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var colAnalyteConcentration =
documentGridForm.FindColumn(PropertyPath.Root.Property("AnalyteConcentration"));
var cell = documentGridForm.DataGridView.Rows[iRow].Cells[colAnalyteConcentration.Index];
documentGridForm.DataGridView.CurrentCell = cell;
cell.Value = concentrations[iRow];
});
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
}
PauseForScreenShot("Document grid with concentrations filled in", 13);
// View the calibration curve p. 13
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
PauseForScreenShot("View calibration curve", 14);
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
}
public QuantificationResult GetQuantification()
{
CalibrationCurveFitter curveFitter = Peptide.GetCalibrationCurveFitter();
return(curveFitter.GetQuantificationResult(ResultFile.Replicate.ReplicateIndex));
}
private void DisplayCalibrationCurve()
{
Text = TabText = _originalFormTitle;
CalibrationCurveOptions options = Settings.Default.CalibrationCurveOptions;
zedGraphControl.GraphPane.YAxis.Type = options.LogYAxis ? AxisType.Log : AxisType.Linear;
zedGraphControl.GraphPane.XAxis.Type = options.LogXAxis ? AxisType.Log : AxisType.Linear;
bool logPlot = options.LogXAxis || options.LogYAxis;
zedGraphControl.GraphPane.Legend.IsVisible = options.ShowLegend;
_scatterPlots = null;
CalibrationCurve = null;
FiguresOfMerit = FiguresOfMerit.EMPTY;
SrmDocument document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available;
return;
}
PeptideDocNode peptide;
PeptideGroupDocNode peptideGroup;
if (!TryGetSelectedPeptide(out peptideGroup, out peptide))
{
zedGraphControl.GraphPane.Title.Text =
ModeUIAwareStringFormat(QuantificationStrings
.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve);
return;
}
if (-1 == document.Children.IndexOf(peptideGroup))
{
zedGraphControl.GraphPane.Title.Text = ModeUIAwareStringFormat(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_peptide_is_no_longer_part_of_the_Skyline_document_);
return;
}
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(document, peptideGroup,
peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
if (curveFitter.IsEnableSingleBatch && Settings.Default.CalibrationCurveOptions.SingleBatch)
{
curveFitter.SingleBatchReplicateIndex = _skylineWindow.SelectedResultsIndex;
}
Text = TabText = GetFormTitle(curveFitter);
if (peptideQuantifier.QuantificationSettings.RegressionFit == RegressionFit.NONE)
{
if (!(peptideQuantifier.NormalizationMethod is NormalizationMethod.RatioToLabel))
{
zedGraphControl.GraphPane.Title.Text =
ModeUIAwareStringFormat(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_);
}
else
{
if (!peptide.InternalStandardConcentration.HasValue)
{
zedGraphControl.GraphPane.Title.Text =
ModeUIAwareStringFormat(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_convert_peak_area_ratios_to_concentrations__specify_the_internal_standard_concentration_for__0__, peptide);
}
else
{
zedGraphControl.GraphPane.Title.Text = null;
}
}
}
else
{
if (curveFitter.GetStandardConcentrations().Any())
{
zedGraphControl.GraphPane.Title.Text = null;
}
else
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_fit_a_calibration_curve__set_the_Sample_Type_of_some_replicates_to_Standard__and_specify_their_concentration_;
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = curveFitter.GetXAxisTitle();
zedGraphControl.GraphPane.YAxis.Title.Text = curveFitter.GetYAxisTitle();
CalibrationCurve = curveFitter.GetCalibrationCurve();
FiguresOfMerit = curveFitter.GetFiguresOfMerit(CalibrationCurve);
double minX = double.MaxValue, maxX = double.MinValue;
double minY = double.MaxValue;
_scatterPlots = new CurveList();
IEnumerable <SampleType> sampleTypes = SampleType.ListSampleTypes()
.Where(Options.DisplaySampleType);
foreach (var sampleType in sampleTypes)
{
PointPairList pointPairList = new PointPairList();
PointPairList pointPairListExcluded = new PointPairList();
foreach (var standardIdentifier in curveFitter.EnumerateCalibrationPoints())
{
if (!Equals(sampleType, curveFitter.GetSampleType(standardIdentifier)))
{
continue;
}
double?y = curveFitter.GetYValue(standardIdentifier);
double?xCalculated = curveFitter.GetCalculatedXValue(CalibrationCurve, standardIdentifier);
double?x = curveFitter.GetSpecifiedXValue(standardIdentifier)
?? xCalculated;
if (y.HasValue && x.HasValue)
{
PointPair point = new PointPair(x.Value, y.Value)
{
Tag = standardIdentifier
};
if (sampleType.AllowExclude && null == standardIdentifier.LabelType && peptide.IsExcludeFromCalibration(standardIdentifier.ReplicateIndex))
{
pointPairListExcluded.Add(point);
}
else
{
pointPairList.Add(point);
}
if (!IsNumber(x) || !IsNumber(y))
{
continue;
}
if (!logPlot || x.Value > 0)
{
minX = Math.Min(minX, x.Value);
}
if (!logPlot || y.Value > 0)
{
minY = Math.Min(minY, y.Value);
}
maxX = Math.Max(maxX, x.Value);
if (IsNumber(xCalculated))
{
maxX = Math.Max(maxX, xCalculated.Value);
if (!logPlot || xCalculated.Value > 0)
{
minX = Math.Min(minX, xCalculated.Value);
}
}
}
}
if (pointPairList.Any())
{
var lineItem = zedGraphControl.GraphPane.AddCurve(sampleType.ToString(), pointPairList,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
lineItem.Symbol.Fill = new Fill(sampleType.Color);
_scatterPlots.Add(lineItem);
}
if (pointPairListExcluded.Any())
{
string curveLabel = pointPairList.Any() ? null : sampleType.ToString();
var lineItem = zedGraphControl.GraphPane.AddCurve(curveLabel, pointPairListExcluded,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
_scatterPlots.Add(lineItem);
}
}
List <string> labelLines = new List <String>();
RegressionFit regressionFit = document.Settings.PeptideSettings.Quantification.RegressionFit;
if (regressionFit != RegressionFit.NONE)
{
if (minX <= maxX)
{
int interpolatedLinePointCount = 100;
if (!logPlot && regressionFit != RegressionFit.LINEAR_IN_LOG_SPACE)
{
if (regressionFit == RegressionFit.LINEAR_THROUGH_ZERO)
{
minX = Math.Min(0, minX);
}
if (regressionFit != RegressionFit.QUADRATIC)
{
interpolatedLinePointCount = 2;
}
}
double[] xValues;
if (CalibrationCurve.TurningPoint.HasValue)
{
xValues = new[] { minX, CalibrationCurve.TurningPoint.Value, maxX };
}
else
{
xValues = new[] { minX, maxX };
}
Array.Sort(xValues);
LineItem interpolatedLine = CreateInterpolatedLine(CalibrationCurve, xValues,
interpolatedLinePointCount, logPlot);
if (null != interpolatedLine)
{
zedGraphControl.GraphPane.CurveList.Add(interpolatedLine);
}
}
labelLines.Add(CalibrationCurve.ToString());
if (CalibrationCurve.RSquared.HasValue)
{
labelLines.Add(CalibrationCurve.RSquaredDisplayText(CalibrationCurve.RSquared.Value));
}
if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
{
labelLines.Add(string.Format(@"{0}: {1}",
QuantificationStrings.Weighting, curveFitter.QuantificationSettings.RegressionWeighting));
}
if (options.ShowFiguresOfMerit)
{
string strFiguresOfMerit = FiguresOfMerit.ToString();
if (!string.IsNullOrEmpty(strFiguresOfMerit))
{
labelLines.Add(strFiguresOfMerit);
}
}
}
CalibrationPoint?selectionIdentifier = null;
if (options.ShowSelection)
{
if (curveFitter.IsotopologResponseCurve)
{
var labelType = (_skylineWindow.SequenceTree.SelectedNode as SrmTreeNode)
?.GetNodeOfType <TransitionGroupTreeNode>()?.DocNode.LabelType;
if (labelType != null)
{
selectionIdentifier =
new CalibrationPoint(_skylineWindow.SelectedResultsIndex,
labelType);
}
}
else
{
selectionIdentifier =
new CalibrationPoint(_skylineWindow.SelectedResultsIndex, null);
}
}
if (selectionIdentifier.HasValue)
{
double?ySelected = curveFitter.GetYValue(selectionIdentifier.Value);
if (IsNumber(ySelected))
{
double? xSelected = curveFitter.GetCalculatedXValue(CalibrationCurve, selectionIdentifier.Value);
var selectedLineColor = Color.FromArgb(128, GraphSummary.ColorSelected);
const float selectedLineWidth = 2;
double? xSpecified = curveFitter.GetSpecifiedXValue(selectionIdentifier.Value);
if (IsNumber(xSelected))
{
ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
var verticalLine = new LineObj(xSelected.Value, ySelected.Value, xSelected.Value,
options.LogYAxis ? minY / 10 : 0)
{
Line = { Color = selectedLineColor, Width = selectedLineWidth },
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
};
zedGraphControl.GraphPane.GraphObjList.Add(verticalLine);
if (IsNumber(xSpecified))
{
var horizontalLine = new LineObj(xSpecified.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = selectedLineColor, Width = selectedLineWidth },
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
};
zedGraphControl.GraphPane.GraphObjList.Add(horizontalLine);
}
}
else
{
// We were not able to map the observed intensity back to the calibration curve, but we still want to
// indicate where the currently selected point is.
if (IsNumber(xSpecified))
{
// If the point has a specified concentration, then use that.
ArrowObj arrow = new ArrowObj(xSpecified.Value, ySelected.Value, xSpecified.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
}
else
{
// Otherwise, draw a horizontal line at the appropriate y-value.
var horizontalLine = new LineObj(minX, ySelected.Value, maxX, ySelected.Value)
{
Line = { Color = selectedLineColor, Width = selectedLineWidth },
Location = { CoordinateFrame = CoordType.AxisXYScale },
IsClippedToChartRect = true,
};
ZedGraphControl.GraphPane.GraphObjList.Add(horizontalLine);
}
}
}
QuantificationResult quantificationResult = null;
double?calculatedConcentration;
if (curveFitter.IsotopologResponseCurve)
{
calculatedConcentration =
curveFitter.GetCalculatedConcentration(CalibrationCurve, selectionIdentifier.Value);
}
else
{
quantificationResult = curveFitter.GetPeptideQuantificationResult(selectionIdentifier.Value.ReplicateIndex);
calculatedConcentration = quantificationResult?.CalculatedConcentration;
}
if (calculatedConcentration.HasValue)
{
labelLines.Add(string.Format(@"{0} = {1}",
QuantificationStrings.Calculated_Concentration,
QuantificationResult.FormatCalculatedConcentration(calculatedConcentration.Value,
curveFitter.QuantificationSettings.Units)));
}
else if (quantificationResult != null && !quantificationResult.NormalizedArea.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_replicate_has_missing_or_truncated_transitions);
}
}
if (Options.ShowFiguresOfMerit)
{
if (IsNumber(FiguresOfMerit.LimitOfDetection))
{
var lodLine = new LineObj(Color.DarkMagenta, FiguresOfMerit.LimitOfDetection.Value, 0,
FiguresOfMerit.LimitOfDetection.Value, 1)
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
};
zedGraphControl.GraphPane.GraphObjList.Add(lodLine);
}
if (IsNumber(FiguresOfMerit.LimitOfQuantification))
{
var loqLine = new LineObj(Color.DarkCyan, FiguresOfMerit.LimitOfQuantification.Value, 0,
FiguresOfMerit.LimitOfQuantification.Value, 1)
{
Location = { CoordinateFrame = CoordType.XScaleYChartFraction }
};
zedGraphControl.GraphPane.GraphObjList.Add(loqLine);
}
}
if (labelLines.Any())
{
TextObj text = new TextObj(TextUtil.LineSeparate(labelLines), .01, 0,
CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
zedGraphControl.GraphPane.GraphObjList.Add(text);
}
}
private void DisplayCalibrationCurve()
{
CalibrationCurveOptions options = Settings.Default.CalibrationCurveOptions;
zedGraphControl.GraphPane.YAxis.Type = zedGraphControl.GraphPane.XAxis.Type
= options.LogPlot ? AxisType.Log : AxisType.Linear;
zedGraphControl.GraphPane.Legend.IsVisible = options.ShowLegend;
_scatterPlots = null;
CalibrationCurve = null;
FiguresOfMerit = FiguresOfMerit.EMPTY;
SrmDocument document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available;
return;
}
PeptideDocNode peptide;
PeptideGroupDocNode peptideGroup;
if (!TryGetSelectedPeptide(out peptideGroup, out peptide))
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings
.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve;
return;
}
if (-1 == document.Children.IndexOf(peptideGroup))
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_peptide_is_no_longer_part_of_the_Skyline_document_;
return;
}
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(document, peptideGroup,
peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
if (peptideQuantifier.QuantificationSettings.RegressionFit == RegressionFit.NONE)
{
if (!(peptideQuantifier.NormalizationMethod is NormalizationMethod.RatioToLabel))
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_;
}
else
{
if (!peptide.InternalStandardConcentration.HasValue)
{
zedGraphControl.GraphPane.Title.Text =
string.Format(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_convert_peak_area_ratios_to_concentrations__specify_the_internal_standard_concentration_for__0__, peptide);
}
else
{
zedGraphControl.GraphPane.Title.Text = null;
}
}
}
else
{
if (curveFitter.GetStandardConcentrations().Any())
{
zedGraphControl.GraphPane.Title.Text = null;
}
else
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_fit_a_calibration_curve__set_the_Sample_Type_of_some_replicates_to_Standard__and_specify_their_concentration_;
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = curveFitter.GetXAxisTitle();
zedGraphControl.GraphPane.YAxis.Title.Text = curveFitter.GetYAxisTitle();
CalibrationCurve = curveFitter.GetCalibrationCurve();
FiguresOfMerit = curveFitter.GetFiguresOfMerit(CalibrationCurve);
double minX = double.MaxValue, maxX = double.MinValue;
double minY = double.MaxValue;
_scatterPlots = new CurveList();
foreach (var sampleType in SampleType.ListSampleTypes())
{
if (!Options.DisplaySampleType(sampleType))
{
continue;
}
PointPairList pointPairList = new PointPairList();
PointPairList pointPairListExcluded = new PointPairList();
for (int iReplicate = 0;
iReplicate < document.Settings.MeasuredResults.Chromatograms.Count;
iReplicate++)
{
ChromatogramSet chromatogramSet = document.Settings.MeasuredResults.Chromatograms[iReplicate];
if (!Equals(sampleType, chromatogramSet.SampleType))
{
continue;
}
double?y = curveFitter.GetYValue(iReplicate);
double?xCalculated = curveFitter.GetCalculatedXValue(CalibrationCurve, iReplicate);
double?x = curveFitter.GetSpecifiedXValue(iReplicate)
?? xCalculated;
if (y.HasValue && x.HasValue)
{
PointPair point = new PointPair(x.Value, y.Value)
{
Tag = iReplicate
};
if (sampleType.AllowExclude && peptide.IsExcludeFromCalibration(iReplicate))
{
pointPairListExcluded.Add(point);
}
else
{
pointPairList.Add(point);
}
if (double.IsNaN(x.Value) || double.IsInfinity(x.Value) ||
double.IsNaN(y.Value) || double.IsInfinity(y.Value))
{
continue;
}
if (!Options.LogPlot || x.Value > 0)
{
minX = Math.Min(minX, x.Value);
}
if (!Options.LogPlot || y.Value > 0)
{
minY = Math.Min(minY, y.Value);
}
maxX = Math.Max(maxX, x.Value);
if (xCalculated.HasValue)
{
maxX = Math.Max(maxX, xCalculated.Value);
if (!Options.LogPlot || xCalculated.Value > 0)
{
minX = Math.Min(minX, xCalculated.Value);
}
}
}
}
if (pointPairList.Any())
{
var lineItem = zedGraphControl.GraphPane.AddCurve(sampleType.ToString(), pointPairList,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
lineItem.Symbol.Fill = new Fill(sampleType.Color);
_scatterPlots.Add(lineItem);
}
if (pointPairListExcluded.Any())
{
string curveLabel = pointPairList.Any() ? null : sampleType.ToString();
var lineItem = zedGraphControl.GraphPane.AddCurve(curveLabel, pointPairListExcluded,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
_scatterPlots.Add(lineItem);
}
}
List <string> labelLines = new List <String>();
RegressionFit regressionFit = document.Settings.PeptideSettings.Quantification.RegressionFit;
if (regressionFit != RegressionFit.NONE)
{
if (minX <= maxX)
{
int interpolatedLinePointCount = 100;
if (!options.LogPlot)
{
if (regressionFit == RegressionFit.LINEAR_THROUGH_ZERO)
{
minX = Math.Min(0, minX);
}
if (regressionFit != RegressionFit.QUADRATIC)
{
interpolatedLinePointCount = 2;
}
}
double[] xValues;
if (CalibrationCurve.TurningPoint.HasValue)
{
xValues = new[] { minX, CalibrationCurve.TurningPoint.Value, maxX };
}
else
{
xValues = new[] { minX, maxX };
}
Array.Sort(xValues);
LineItem interpolatedLine = CreateInterpolatedLine(CalibrationCurve, xValues,
interpolatedLinePointCount, Options.LogPlot);
if (null != interpolatedLine)
{
zedGraphControl.GraphPane.CurveList.Add(interpolatedLine);
}
}
labelLines.Add(CalibrationCurve.ToString());
if (CalibrationCurve.RSquared.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_ +
CalibrationCurve.RSquared.Value.ToString("0.####")); // Not L10N
}
if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
{
labelLines.Add(string.Format("{0}: {1}", // Not L10N
QuantificationStrings.Weighting, curveFitter.QuantificationSettings.RegressionWeighting));
}
string strFiguresOfMerit = FiguresOfMerit.ToString();
if (!string.IsNullOrEmpty(strFiguresOfMerit))
{
labelLines.Add(strFiguresOfMerit);
}
}
if (options.ShowSelection)
{
double?ySelected = curveFitter.GetYValue(_skylineWindow.SelectedResultsIndex);
double?xSelected = curveFitter.GetCalculatedXValue(CalibrationCurve, _skylineWindow.SelectedResultsIndex);
if (xSelected.HasValue && ySelected.HasValue)
{
const float selectedLineWidth = 2;
ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
var selectedLineColor = Color.FromArgb(128, GraphSummary.ColorSelected);
var verticalLine = new LineObj(xSelected.Value, ySelected.Value, xSelected.Value, options.LogPlot ? double.MinValue : 0)
{
Line = { Color = selectedLineColor, Width = selectedLineWidth },
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
};
zedGraphControl.GraphPane.GraphObjList.Add(verticalLine);
double?xSpecified = curveFitter.GetSpecifiedXValue(_skylineWindow.SelectedResultsIndex);
if (xSpecified.HasValue)
{
var horizontalLine = new LineObj(xSpecified.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = selectedLineColor, Width = selectedLineWidth },
Location = { CoordinateFrame = CoordType.AxisXYScale },
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
};
zedGraphControl.GraphPane.GraphObjList.Add(horizontalLine);
}
}
var quantificationResult = curveFitter.GetQuantificationResult(_skylineWindow.SelectedResultsIndex);
if (quantificationResult.CalculatedConcentration.HasValue)
{
labelLines.Add(string.Format("{0} = {1}", // Not L10N
QuantificationStrings.Calculated_Concentration, quantificationResult));
}
else if (!quantificationResult.NormalizedArea.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_replicate_has_missing_or_truncated_transitions);
}
}
if (labelLines.Any())
{
TextObj text = new TextObj(TextUtil.LineSeparate(labelLines), .01, 0,
CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
zedGraphControl.GraphPane.GraphObjList.Add(text);
}
}
private void DisplayCalibrationCurve()
{
CalibrationCurveOptions options = Settings.Default.CalibrationCurveOptions;
zedGraphControl.GraphPane.YAxis.Type = zedGraphControl.GraphPane.XAxis.Type
= options.LogPlot ? AxisType.Log : AxisType.Linear;
zedGraphControl.GraphPane.Legend.IsVisible = options.ShowLegend;
_scatterPlots = null;
CalibrationCurve = null;
SrmDocument document = DocumentUiContainer.DocumentUI;
if (!document.Settings.HasResults)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_No_results_available;
return;
}
PeptideDocNode peptide = null;
PeptideGroupDocNode peptideGroup = null;
SequenceTree sequenceTree = _skylineWindow.SequenceTree;
if (null != sequenceTree)
{
PeptideTreeNode peptideTreeNode = sequenceTree.GetNodeOfType <PeptideTreeNode>();
if (null != peptideTreeNode)
{
peptide = peptideTreeNode.DocNode;
}
PeptideGroupTreeNode peptideGroupTreeNode = sequenceTree.GetNodeOfType <PeptideGroupTreeNode>();
if (null != peptideGroupTreeNode)
{
peptideGroup = peptideGroupTreeNode.DocNode;
}
}
if (null == peptide)
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings
.CalibrationForm_DisplayCalibrationCurve_Select_a_peptide_to_see_its_calibration_curve;
return;
}
PeptideQuantifier peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(document.Settings, peptideGroup,
peptide);
CalibrationCurveFitter curveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
if (peptideQuantifier.QuantificationSettings.RegressionFit == RegressionFit.NONE)
{
if (string.IsNullOrEmpty(
peptideQuantifier.QuantificationSettings.NormalizationMethod.IsotopeLabelTypeName))
{
zedGraphControl.GraphPane.Title.Text =
QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_Use_the_Quantification_tab_on_the_Peptide_Settings_dialog_to_control_the_conversion_of_peak_areas_to_concentrations_;
}
else
{
if (!peptide.InternalStandardConcentration.HasValue)
{
zedGraphControl.GraphPane.Title.Text =
string.Format(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_convert_peak_area_ratios_to_concentrations__specify_the_internal_standard_concentration_for__0__, peptide);
}
else
{
zedGraphControl.GraphPane.Title.Text = null;
}
}
}
else
{
if (curveFitter.GetStandardConcentrations().Any())
{
zedGraphControl.GraphPane.Title.Text = null;
}
else
{
zedGraphControl.GraphPane.Title.Text = QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_To_fit_a_calibration_curve__set_the_Sample_Type_of_some_replicates_to_Standard__and_specify_their_concentration_;
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = curveFitter.GetXAxisTitle();
zedGraphControl.GraphPane.YAxis.Title.Text = curveFitter.GetYAxisTitle();
CalibrationCurve = curveFitter.GetCalibrationCurve();
double minX = double.MaxValue, maxX = double.MinValue;
_scatterPlots = new CurveList();
foreach (var sampleType in SampleType.ListSampleTypes())
{
if (!Options.DisplaySampleType(sampleType))
{
continue;
}
PointPairList pointPairList = new PointPairList();
for (int iReplicate = 0;
iReplicate < document.Settings.MeasuredResults.Chromatograms.Count;
iReplicate++)
{
ChromatogramSet chromatogramSet = document.Settings.MeasuredResults.Chromatograms[iReplicate];
if (!Equals(sampleType, chromatogramSet.SampleType))
{
continue;
}
double?y = curveFitter.GetYValue(iReplicate);
double?x = curveFitter.GetSpecifiedXValue(iReplicate)
?? curveFitter.GetCalculatedXValue(CalibrationCurve, iReplicate);
if (y.HasValue && x.HasValue)
{
PointPair point = new PointPair(x.Value, y.Value)
{
Tag = iReplicate
};
pointPairList.Add(point);
if (!Options.LogPlot || x.Value > 0)
{
minX = Math.Min(minX, x.Value);
}
maxX = Math.Max(maxX, x.Value);
}
}
if (pointPairList.Any())
{
var lineItem = zedGraphControl.GraphPane.AddCurve(sampleType.ToString(), pointPairList,
sampleType.Color, sampleType.SymbolType);
lineItem.Line.IsVisible = false;
lineItem.Symbol.Fill = new Fill(sampleType.Color);
_scatterPlots.Add(lineItem);
}
}
List <string> labelLines = new List <String>();
RegressionFit regressionFit = document.Settings.PeptideSettings.Quantification.RegressionFit;
if (regressionFit != RegressionFit.NONE)
{
if (minX <= maxX)
{
int interpolatedLinePointCount = 100;
if (!options.LogPlot)
{
if (regressionFit == RegressionFit.LINEAR_THROUGH_ZERO)
{
minX = Math.Min(0, minX);
}
if (regressionFit != RegressionFit.QUADRATIC)
{
interpolatedLinePointCount = 2;
}
}
LineItem interpolatedLine = CreateInterpolatedLine(CalibrationCurve, minX, maxX,
interpolatedLinePointCount, Options.LogPlot);
if (null != interpolatedLine)
{
zedGraphControl.GraphPane.CurveList.Add(interpolatedLine);
}
}
labelLines.Add(CalibrationCurve.ToString());
if (CalibrationCurve.RSquared.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_ +
CalibrationCurve.RSquared.Value.ToString("0.####")); // Not L10N
}
if (!Equals(curveFitter.QuantificationSettings.RegressionWeighting, RegressionWeighting.NONE))
{
labelLines.Add(string.Format("{0}: {1}", // Not L10N
QuantificationStrings.Weighting, curveFitter.QuantificationSettings.RegressionWeighting));
}
}
if (options.ShowSelection)
{
double?ySelected = curveFitter.GetYValue(_skylineWindow.SelectedResultsIndex);
double?xSelected = curveFitter.GetCalculatedXValue(CalibrationCurve, _skylineWindow.SelectedResultsIndex);
if (xSelected.HasValue && ySelected.HasValue)
{
ArrowObj arrow = new ArrowObj(xSelected.Value, ySelected.Value, xSelected.Value,
ySelected.Value)
{
Line = { Color = GraphSummary.ColorSelected }
};
zedGraphControl.GraphPane.GraphObjList.Insert(0, arrow);
}
var quantificationResult = curveFitter.GetQuantificationResult(_skylineWindow.SelectedResultsIndex);
if (quantificationResult.CalculatedConcentration.HasValue)
{
labelLines.Add(string.Format("{0} = {1}", // Not L10N
QuantificationStrings.Calculated_Concentration, quantificationResult));
}
else if (!quantificationResult.NormalizedArea.HasValue)
{
labelLines.Add(QuantificationStrings.CalibrationForm_DisplayCalibrationCurve_The_selected_replicate_has_missing_or_truncated_transitions);
}
}
if (labelLines.Any())
{
TextObj text = new TextObj(TextUtil.LineSeparate(labelLines), .01, 0,
CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
zedGraphControl.GraphPane.GraphObjList.Add(text);
}
}
protected override void DoTest()
{
RunUI(() =>
{
SkylineWindow.ResetDefaultSettings();
SkylineWindow.NewDocument();
});
ShowAndPositionAuditLog(false);
PauseForScreenShot <AuditLogForm>("Empty Audit Log form.", 2);
// Configuring Settings for Inserting a New Peptide, p. 3
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
PeptideSettingsUI peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUi);
RunUI(() => peptideSettingsUi.PickedHeavyMods = new[] { modHeavyK.Name });
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with settings modifications.", 4);
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.Width = 1010;
});
PauseForScreenShot("Undo list expanded. (manual)", 4);
RunUI(SkylineWindow.Undo);
PauseForScreenShot("Redo list expanded. (manual)", 5);
RunUI(SkylineWindow.Redo);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
RunUI(pasteDlg.PastePeptides);
RunUI(() =>
{
pasteDlg.Size = new Size(700, 210);
pasteDlg.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
using (new WaitDocumentChange())
{
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
WaitForConditionUI(() => SkylineWindow.SequenceTree.Nodes.Count > 0);
}
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Height = 390;
});
PauseForScreenShot("Main window with Targets view", 6);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with inserted peptide.", 7);
ShowLastExtraInfo("Extra info form with inserted peptide info.", 7);
string documentPath = GetTestPath("AuditLogTutorial" + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentPath));
WaitForCondition(() => File.Exists(documentPath));
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value;
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
OkDialog(importResultsDlg, importResultsDlg.OkDialog);
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(9, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <AuditLogForm>("Audit Log form with imported data files.", 9);
ShowLastExtraInfo("Extra info form for the import.", 9);
// Peptide Quantitification Settings p. 9
peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = (PeptideSettingsUI.TABS) 5);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with quantification settings.", 10);
// Specify analyte concentrations of external standards
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.ShowDocumentGrid(true);
});
var documentGridForm = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
string pasteString = TextUtil.LineSeparate(concentrations.Select((f, i) =>
QuantificationStrings.SampleType_STANDARD_Standard + "\t" + f));
ClipboardEx.SetText(pasteString);
using (new WaitDocumentChange())
{
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.CurrentCell = documentGridForm.DataGridView.Rows[1].Cells[colSampleType.Index];
documentGridForm.DataGridView.SendPaste();
});
}
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var gridFloatingWindow = documentGridForm.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 315);
gridFloatingWindow.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <DocumentGridForm>("Document grid with concentrations filled in", 11);
RunUI(documentGridForm.Close);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with grid changes", 12);
ShowLastExtraInfo("Extra Info for the analyte data import.", 12);
RunUI(SkylineWindow.AuditLogForm.Close);
const string unknownReplicate = "FOXN1-GST";
RestoreViewOnScreen(13);
ActivateReplicate(unknownReplicate);
SelectNode(SrmDocument.Level.TransitionGroups, 1);
RunUI(() => SkylineWindow.Size = new Size(936, 527));
WaitForGraphs();
PauseForScreenShot("Heavy precursor chromatogram", 13);
RunUI(() =>
{
var pathHeavy = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1);
var graphChrom = SkylineWindow.GetGraphChrom(unknownReplicate);
Assert.IsNotNull(graphChrom);
Assert.AreEqual(unknownReplicate, graphChrom.NameSet);
var firstGroupInfo = graphChrom.ChromGroupInfos.FirstOrDefault();
Assert.IsNotNull(firstGroupInfo, "Missing group info");
var firstChromItem = graphChrom.GraphItems.FirstOrDefault(gci => gci.TransitionChromInfo != null);
Assert.IsNotNull(firstChromItem, "Missing graph item");
var listChanges = new List <ChangedPeakBoundsEventArgs>
{
new ChangedPeakBoundsEventArgs(pathHeavy,
null,
graphChrom.NameSet,
firstGroupInfo.FilePath,
firstChromItem.GetValidPeakBoundaryTime(20.65),
firstChromItem.GetValidPeakBoundaryTime(21.15),
PeakIdentification.FALSE,
PeakBoundsChangeType.both)
};
graphChrom.SimulateChangedPeakBounds(listChanges);
});
ShowAndPositionAuditLog(true, 50, 200);
WaitForConditionUI(500, () => SkylineWindow.AuditLogForm.DataGridView.Rows.Count > 0);
PauseForScreenShot <AuditLogForm>("Audit Log form with changed integration boundary.", 14);
int reasonIndex = 2;
using (new WaitDocumentChange())
{
RunUI(() =>
{
var pathReason = PropertyPath.Root.Property("Reason");
var colReason = SkylineWindow.AuditLogForm.FindColumn(pathReason);
reasonIndex = colReason.Index;
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex,
"Changed peak integration as instructed by the tutorial");
});
}
RunUI(() => SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex));
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
PauseForScreenShot <AuditLogForm>("Audit Log form with updated reason.", 14);
// View the calibration curve p. 15
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
var priorZoomState = ZoomCalibrationCurve(calibrationForm, 0.52);
RunUI(() =>
{
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
VerifyCalibrationCurve(calibrationForm, 5.4065E-1, -2.9539E-1, 0.999);
});
PauseForScreenShot <CalibrationForm>("Calibration curve zoomed", 15);
RunUI(() =>
{
priorZoomState?.ApplyState(calibrationForm.ZedGraphControl.GraphPane);
var chromatograms = SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms;
new [] { 5, 6, 7, 8 }.ForEach((index) =>
{
int replicateIdx = chromatograms.IndexOf((ch) => ch.Name.Equals("Standard_" + index));
Assert.IsTrue(replicateIdx >= 0);
using (var excludeStandardMenu = calibrationForm.MakeExcludeStandardMenuItem(replicateIdx))
{
excludeStandardMenu?.PerformClick();
}
});
});
WaitForGraphs();
RunUI(() => VerifyCalibrationCurve(calibrationForm, 5.52E-1, -6.3678E-1, 1));
OkDialog(calibrationForm, calibrationForm.Close);
PauseForScreenShot <AuditLogForm>("Audit Log with excluded standard records", 16);
PauseForScreenShot <AuditLogForm>("Audit Log Reports menu (manual)", 16);
// TODO(nicksh): Audit log reason field does not currently support fill down
// RunUI(() =>
// {
// SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex, "Excluded standard below LOD");
// for (int i = 0; i < 4; i++)
// SkylineWindow.AuditLogForm.DataGridView.Rows[i].Cells[reasonIndex].Selected = true;
// });
// RunUI(() => SkylineWindow.AuditLogForm.DataboundGridControl.FillDown());
RunUI(() =>
{
for (int i = 0; i < 4; i++)
{
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, i, reasonIndex, "Excluded standard below LOD");
}
});
RunUI(() =>
{
SkylineWindow.AuditLogForm.ChooseView(AuditLogStrings.AuditLogForm_MakeAuditLogForm_Undo_Redo);
});
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() =>
{
var floatingWindow = SkylineWindow.AuditLogForm.Parent.Parent;
floatingWindow.Height = 334;
floatingWindow.Width -= 15;
});
PauseForScreenShot <AuditLogForm>("Audit Log with UndoRedo view.", 17);
if (IsCoverShotMode)
{
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
var calibrationCoverForm = WaitForOpenForm <CalibrationForm>();
ZoomCalibrationCurve(calibrationCoverForm, 0.53);
var floatingLogWindow = SkylineWindow.AuditLogForm.Parent.Parent;
var floatingCalWindow = calibrationCoverForm.Parent.Parent;
RunUI(() =>
{
floatingLogWindow.Top = SkylineWindow.Bottom - floatingLogWindow.Height - 8;
floatingLogWindow.Left =
(SkylineWindow.Left + SkylineWindow.Right) / 2 - floatingLogWindow.Width / 2;
floatingCalWindow.Top = SkylineWindow.Top + 8;
floatingCalWindow.Left = SkylineWindow.Right - floatingCalWindow.Width - 8;
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex);
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex - 1);
});
TakeCoverShot();
}
var customizeDialog = ShowDialog <ViewEditor>(SkylineWindow.AuditLogForm.NavBar.CustomizeView);
RunUI(() =>
{
customizeDialog.ViewName = "Custom Columns";
var columnsToAdd = new[]
{
PropertyPath.Parse("SkylineVersion"),
PropertyPath.Parse("User"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(customizeDialog.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
customizeDialog.ChooseColumnsTab.AddSelectedColumn();
}
customizeDialog.Height = 370;
});
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Custom Columns report template", 17);
OkDialog(customizeDialog, customizeDialog.OkDialog);
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() => SkylineWindow.AuditLogForm.Parent.Parent.Height += 10); // Extra for 2-line headers
PauseForScreenShot <AuditLogForm>("Audit Log with custom view.", 18);
var registrationDialog = ShowDialog <MultiButtonMsgDlg>(() => SkylineWindow.ShowPublishDlg(null));
PauseForScreenShot <MultiButtonMsgDlg>("Upload confirmation dialog.", 19);
var loginDialog = ShowDialog <EditServerDlg>(registrationDialog.ClickNo);
PauseForScreenShot <EditServerDlg>("Login dialog.", 20);
RunUI(() =>
{
loginDialog.URL = SERVER_URL;
loginDialog.Username = PANORAMA_USER_NAME;
});
if (!IsPauseForScreenShots)
{
OkDialog(loginDialog, loginDialog.CancelButton.PerformClick);
}
else
{
PauseTest("Enter password. (manual) No screen shot.");
var publishDialog = ShowDialog <PublishDocumentDlg>(loginDialog.OkDialog);
WaitForCondition(() => publishDialog.IsLoaded);
RunUI(() =>
{
publishDialog.SelectItem(testFolderName);
});
PauseForScreenShot <PublishDocumentDlg>("Folder selection dialog.", 21);
var browserConfirmationDialog = ShowDialog <MultiButtonMsgDlg>(publishDialog.OkDialog);
OkDialog(browserConfirmationDialog, browserConfirmationDialog.ClickYes);
PauseForScreenShot("Uploaded document in Panorama (in browser).");
Regex reDocId = new Regex(@"\?id=([0-9]+)");
Assert.IsTrue(reDocId.IsMatch(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()));
string docId = reDocId.Match(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()).Groups[1].Captures[0].Value;
Uri serverUri = new Uri(SERVER_URL);
Uri requestUri = PanoramaUtil.Call(serverUri, "targetedms", String.Format("{0}/{1}", PANORAMA_FOLDER, testFolderName),
"showSkylineAuditLog", "id=" + docId);
Process.Start(requestUri.ToString());
PauseForScreenShot("Uploaded document audit log in Panorama (in browser).");
}
}
protected override void DoTest()
{
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("p180test_calibration_DukeApril2016.sky")));
var surrogateStandards = new Dictionary <string, string>
{
{ "Leu", "Ile" },
{ "Lys", "Orn" },
{ "Ac-Orn", "Orn" },
{ "SDMA", "ADMA" },
{ "alpha-AAA", "Orn" },
{ "Carnosine", "His" },
{ "Histamine", "His" },
{ "Kynurenine", "Tyr" },
{ "Met-SO", "Met" },
{ "Nitro-Tyr", "Tyr" },
{ "c4-OH-Pro", "Pro" },
{ "t4-OH-Pro", "Pro" },
};
// Set the standard type of the surrogate standards to StandardType.SURROGATE_STANDARD
RunUI(() =>
{
List <IdentityPath> pathsToSelect = SkylineWindow.SequenceTree.Nodes.OfType <PeptideGroupTreeNode>()
.SelectMany(peptideGroup => peptideGroup.Nodes.OfType <PeptideTreeNode>())
.Where(peptideTreeNode => surrogateStandards.Values.Contains(peptideTreeNode.DocNode.RawTextId))
.Select(treeNode => treeNode.Path)
.ToList();
SkylineWindow.SequenceTree.SelectedPaths = pathsToSelect;
SkylineWindow.SetStandardType(StandardType.SURROGATE_STANDARD);
});
// Use the document grid to set the Normalization Method of the molecules that have surrogate standards
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification));
IDataGridViewEditingControl editingControl = null;
DataGridViewEditingControlShowingEventHandler onEditingControlShowing =
(sender, args) => editingControl = args.Control as IDataGridViewEditingControl;
documentGrid.DataGridView.EditingControlShowing += onEditingControlShowing;
// ReSharper disable AccessToForEachVariableInClosure
foreach (var entry in surrogateStandards)
{
WaitForConditionUI(() => documentGrid.IsComplete);
RunUI(() =>
{
var colPeptide = documentGrid.FindColumn(PropertyPath.Root);
for (int iRow = 0; iRow < documentGrid.RowCount; iRow++)
{
var row = documentGrid.DataGridView.Rows[iRow];
if (!entry.Key.Equals(row.Cells[colPeptide.Index].FormattedValue))
{
continue;
}
var colNormalizationMethod = documentGrid.FindColumn(PropertyPath.Root.Property("NormalizationMethod"));
documentGrid.DataGridView.CurrentCell = row.Cells[colNormalizationMethod.Index];
documentGrid.DataGridView.BeginEdit(false);
editingControl.EditingControlFormattedValue =
string.Format(Resources.RatioToSurrogate_ToString_Ratio_to_surrogate__0____1__, entry.Value,
"Heavy");
documentGrid.DataGridView.EndEdit();
}
});
}
// Make sure that the Y-Axis on the CalibrationForm reflects the normalization method of the selected molecule
var calibrationForm = ShowDialog <CalibrationForm>(() => SkylineWindow.ShowCalibrationForm());
foreach (var peptideGroupTreeNode in SkylineWindow.SequenceTree.Nodes.OfType <PeptideGroupTreeNode>())
{
foreach (var peptideTreeNode in peptideGroupTreeNode.Nodes.OfType <PeptideTreeNode>())
{
RunUI(() => SkylineWindow.SequenceTree.SelectedPath = peptideTreeNode.Path);
WaitForGraphs();
string yAxisText = calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text;
if (null != peptideTreeNode.DocNode.NormalizationMethod)
{
Assert.IsInstanceOfType(peptideTreeNode.DocNode.NormalizationMethod, typeof(NormalizationMethod.RatioToSurrogate));
Assert.AreEqual(QuantificationStrings.CalibrationCurveFitter_GetYAxisTitle_Normalized_Peak_Area,
yAxisText);
}
else
{
Assert.IsInstanceOfType(SkylineWindow.Document.Settings.PeptideSettings.Quantification.NormalizationMethod, typeof(NormalizationMethod.RatioToLabel));
string expectedTitle = CalibrationCurveFitter.PeakAreaRatioText(IsotopeLabelType.light,
IsotopeLabelType.heavy);
Assert.AreEqual(expectedTitle, yAxisText);
}
}
}
}
public AreaCVRefinementData(SrmDocument document, AreaCVRefinementSettings settings,
CancellationToken token, SrmSettingsChangeMonitor progressMonitor = null)
{
_settings = settings;
if (document == null || !document.Settings.HasResults)
{
return;
}
var replicates = document.MeasuredResults.Chromatograms.Count;
var areas = new List <AreaInfo>(replicates);
var annotations = AnnotationHelper.GetPossibleAnnotations(document, settings.Group).ToArray();
if (!annotations.Any() && settings.Group == null)
{
annotations = new string[] { null }
}
;
_internalData = new List <InternalData>();
var hasHeavyMods = document.Settings.PeptideSettings.Modifications.HasHeavyModifications;
var hasGlobalStandards = document.Settings.HasGlobalStandardArea;
var ms1 = settings.MsLevel == AreaCVMsLevel.precursors;
// Avoid using not-MS1 with a document that is only MS1
if (!ms1 && document.MoleculeTransitions.All(t => t.IsMs1))
{
ms1 = true;
}
double?qvalueCutoff = null;
if (ShouldUseQValues(document))
{
qvalueCutoff = _settings.QValueCutoff;
}
int?minDetections = null;
if (_settings.MinimumDetections != -1)
{
minDetections = _settings.MinimumDetections;
}
MedianInfo medianInfo = null;
int? ratioIndex = null;
if (settings.NormalizeOption.IsRatioToLabel)
{
var isotopeLabelTypeName = (settings.NormalizeOption.NormalizationMethod as NormalizationMethod.RatioToLabel)
?.IsotopeLabelTypeName;
ratioIndex =
document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes.IndexOf(type =>
type.Name == isotopeLabelTypeName);
}
if (_settings.NormalizeOption.Is(NormalizationMethod.EQUALIZE_MEDIANS))
{
medianInfo = CalculateMedianAreas(document);
}
NormalizationData normalizationData = null;
foreach (var peptideGroup in document.MoleculeGroups)
{
foreach (var peptide in peptideGroup.Molecules)
{
if (progressMonitor != null)
{
progressMonitor.ProcessMolecule(peptide);
}
if (_settings.PointsType == PointsTypePeakArea.decoys != peptide.IsDecoy)
{
continue;
}
CalibrationCurveFitter calibrationCurveFitter = null;
CalibrationCurve calibrationCurve = null;
IEnumerable <TransitionGroupDocNode> transitionGroups;
if (_settings.NormalizeOption == NormalizeOption.CALIBRATED ||
_settings.NormalizeOption == NormalizeOption.DEFAULT)
{
if (!peptide.TransitionGroups.Any())
{
continue;
}
var peptideQuantifier = PeptideQuantifier.GetPeptideQuantifier(() =>
{
return(normalizationData = normalizationData ?? NormalizationData.GetNormalizationData(document, false, null));
}, document.Settings, peptideGroup, peptide);
calibrationCurveFitter = new CalibrationCurveFitter(peptideQuantifier, document.Settings);
transitionGroups = new[] { peptide.TransitionGroups.First() };
if (_settings.NormalizeOption == NormalizeOption.CALIBRATED)
{
calibrationCurve = calibrationCurveFitter.GetCalibrationCurve();
if (calibrationCurve == null)
{
continue;
}
}
}
else
{
transitionGroups = peptide.TransitionGroups;
}
foreach (var transitionGroupDocNode in transitionGroups)
{
foreach (var a in annotations)
{
areas.Clear();
if (!Equals(a, _settings.Annotation) && (_settings.Group == null || _settings.Annotation != null))
{
continue;
}
foreach (var replicateIndex in AnnotationHelper.GetReplicateIndices(document,
_settings.Group, a))
{
if (progressMonitor != null && progressMonitor.IsCanceled())
{
throw new OperationCanceledException();
}
token.ThrowIfCancellationRequested();
var groupChromInfo = transitionGroupDocNode.GetSafeChromInfo(replicateIndex)
.FirstOrDefault(c => c.OptimizationStep == 0);
if (groupChromInfo == null)
{
continue;
}
if (qvalueCutoff.HasValue)
{
if (!(groupChromInfo.QValue.HasValue &&
groupChromInfo.QValue.Value < qvalueCutoff.Value))
{
continue;
}
}
double sumArea, normalizedArea;
if (calibrationCurveFitter != null)
{
double?value;
if (calibrationCurve != null)
{
value = calibrationCurveFitter.GetCalculatedConcentration(calibrationCurve,
replicateIndex);
}
else
{
value = calibrationCurveFitter.GetNormalizedPeakArea(
new CalibrationPoint(replicateIndex, null));
}
if (!value.HasValue)
{
continue;
}
sumArea = value.Value;
normalizedArea = value.Value;
}
else
{
if (!groupChromInfo.Area.HasValue)
{
continue;
}
var index = replicateIndex;
sumArea = transitionGroupDocNode.Transitions.Where(t =>
{
if (ms1 != t.IsMs1 || !t.ExplicitQuantitative)
{
return(false);
}
var chromInfo = t.GetSafeChromInfo(index)
.FirstOrDefault(c => c.OptimizationStep == 0);
if (chromInfo == null)
{
return(false);
}
if (_settings.Transitions == AreaCVTransitions.best)
{
return(chromInfo.RankByLevel == 1);
}
if (_settings.Transitions == AreaCVTransitions.all)
{
return(true);
}
return(chromInfo.RankByLevel <= _settings.CountTransitions);
// ReSharper disable once PossibleNullReferenceException
}).Sum(t => (double)t.GetSafeChromInfo(index)
.FirstOrDefault(c => c.OptimizationStep == 0).Area);
normalizedArea = sumArea;
if (_settings.NormalizeOption.Is(NormalizationMethod.EQUALIZE_MEDIANS))
{
normalizedArea /= medianInfo.Medians[replicateIndex] / medianInfo.MedianMedian;
}
else if (_settings.NormalizeOption.Is(NormalizationMethod.GLOBAL_STANDARDS) &&
hasGlobalStandards)
{
normalizedArea =
NormalizeToGlobalStandard(document, transitionGroupDocNode, replicateIndex,
sumArea);
}
else if (_settings.NormalizeOption.Is(NormalizationMethod.TIC))
{
var denominator = document.Settings.GetTicNormalizationDenominator(
replicateIndex, groupChromInfo.FileId);
if (!denominator.HasValue)
{
continue;
}
normalizedArea /= denominator.Value;
}
else if (hasHeavyMods &&
_settings.NormalizeOption.NormalizationMethod is NormalizationMethod
.RatioToLabel)
{
var ci = transitionGroupDocNode.GetSafeChromInfo(replicateIndex)
.FirstOrDefault(c => c.OptimizationStep == 0);
RatioValue ratioValue = null;
if (ratioIndex.HasValue && ratioIndex.Value >= 0 &&
ratioIndex.Value < ci.Ratios.Count)
{
ratioValue = ci.Ratios[ratioIndex.Value];
}
if (ratioValue == null)
{
continue;
}
normalizedArea = ratioValue.Ratio;
}
}
areas.Add(new AreaInfo(sumArea, normalizedArea));
}
if (qvalueCutoff.HasValue && minDetections.HasValue && areas.Count < minDetections.Value)
{
continue;
}
_settings.AddToInternalData(_internalData, areas, peptideGroup, peptide, transitionGroupDocNode, a);
}
}
}
}
Data = ImmutableList <CVData> .ValueOf(_internalData.GroupBy(i => i, (key, grouped) =>
{
var groupedArray = grouped.ToArray();
return(new CVData(
groupedArray.Select(idata => new PeptideAnnotationPair(idata.PeptideGroup, idata.Peptide, idata.TransitionGroup, idata.Annotation, idata.CV)),
key.CVBucketed, key.Area, groupedArray.Length));
}).OrderBy(d => d.CV));
}
