/// <summary>
/// Verify that the order of replicates on the graph is based on the ordering specified by getValueFunc.
/// </summary>
private void VerifyOrder <T>(GraphSummary graphSummary, Func <ChromatogramSet, T> getValueFunc)
{
var document = graphSummary.DocumentUIContainer.Document;
var measuredResults = document.Settings.MeasuredResults;
Assert.IsNotNull(measuredResults);
var summaryReplicateGraphPane = graphSummary.GraphControl.GraphPane as SummaryReplicateGraphPane;
Assert.IsNotNull(summaryReplicateGraphPane);
Assert.IsNotNull(summaryReplicateGraphPane);
int replicateCount = measuredResults.Chromatograms.Count;
Assert.AreEqual(replicateCount, summaryReplicateGraphPane.XAxis.Scale.TextLabels.Length);
var replicates = new List <ChromatogramSet>();
for (int i = 0; i < replicateCount; i++)
{
var replicateIndexSet = summaryReplicateGraphPane.IndexOfReplicate(i);
Assert.AreEqual(1, replicateIndexSet.Count);
replicates.Add(measuredResults.Chromatograms[replicateIndexSet.First()]);
}
for (int i = 1; i < replicates.Count; i++)
{
T prevValue = getValueFunc(replicates[i - 1]);
T curValue = getValueFunc(replicates[i]);
var comparison = Comparer <T> .Default.Compare(prevValue, curValue);
Assert.IsTrue(comparison <= 0);
}
}
public static void CreateAndShowFindResults(ZedGraphControl sender, GraphSummary graphSummary, SrmDocument document, AreaCVGraphData.CVData data)
{
var peptideAnnotationPairs = data.PeptideAnnotationPairs.ToList();
var results = new List <FindResult>(peptideAnnotationPairs.Count);
var pred = new FindPredicate(new FindOptions().ChangeCustomFinders(new[] { new PeptideAnnotationPairFinder(peptideAnnotationPairs, data.CV) }), Program.MainWindow.SequenceTree.GetDisplaySettings(null));
for (var i = 0; i < Math.Min(peptideAnnotationPairs.Count, MAX_FINDRESULTS_PEPTIDES); i++)
{
var pair = peptideAnnotationPairs[i];
var displayText = PeptideAnnotationPairFinder.GetDisplayText(data.CV, pair.Annotation);
results.Add(new FindResult(pred,
new BookmarkEnumerator(document,
new Bookmark(document.GetPathTo((int)SrmDocument.Level.Molecules,
document.Molecules.ToList().IndexOf(pair.Peptide)))), new FindMatch(displayText)));
}
var count = peptideAnnotationPairs.Count;
if (results.Count != count)
{
MessageDlg.Show(sender, string.Format(Resources.HistogramHelper_CreateAndShowFindResults_Only_showing__0___1__peptides, MAX_FINDRESULTS_PEPTIDES, count));
results = results.GetRange(0, MAX_FINDRESULTS_PEPTIDES);
}
if (peptideAnnotationPairs.Count == 1)
{
var nodes = peptideAnnotationPairs[0];
graphSummary.StateProvider.SelectedPath = new IdentityPath(nodes.PeptideGroup.PeptideGroup, nodes.Peptide.Peptide);
}
Program.MainWindow.ShowFindResults(results);
}
private void CheckNonlinearRegressionMethods(GraphSummary summary)
{
//Check rmsd and number of linear functions for KDE
RunUI(() => SkylineWindow.ShowRegressionMethod(RegressionMethodRT.kde));
WaitForPaneCondition <RTLinearRegressionGraphPane>(summary, pane => !pane.IsCalculating);
RTLinearRegressionGraphPane graphPane;
summary.TryGetGraphPane(out graphPane);
//KDE should never be refined. Too slow
Assert.IsFalse(graphPane.IsRefined);
var kdeFunction = (PiecewiseLinearRegressionFunction)graphPane.RegressionRefined.Conversion;
Assert.AreEqual(5.7326, kdeFunction.RMSD, 0.0001);
Assert.AreEqual(22, kdeFunction.LinearFunctionsCount);
//Check for Loess
RunUI(() => SkylineWindow.ShowRegressionMethod(RegressionMethodRT.loess));
WaitForPaneCondition <RTLinearRegressionGraphPane>(summary, pane => !pane.IsCalculating);
//Make sure Loess is not refined. Too slow
Assert.IsTrue(graphPane.RegressionRefinedNull);
// ReSharper disable once PossibleInvalidCastException
var loessFunction = (LoessRegression)graphPane.RegressionRefined.Conversion;
Assert.AreEqual(4.0552, loessFunction.Rmsd, 0.0001);
Assert.AreEqual(22, kdeFunction.LinearFunctionsCount);
}
public void OpenAndChangeAreaCVProperties(GraphSummary graphSummary, Action <AreaCVToolbarProperties> action)
{
RunDlg <AreaCVToolbarProperties>(() => SkylineWindow.ShowAreaCVPropertyDlg(graphSummary), d =>
{
action(d);
d.OK();
});
UpdateGraphAndWait(SkylineWindow.GraphPeakArea);
}
private void VerifyGraphYRange(GraphSummary graphSummary, double minHeight, double maxHeight, int pointCount, int errorCount = 0)
{
RunUI(() =>
{
graphSummary.CountCurves(c =>
{
if (pointCount != CountPoints(c, minHeight, maxHeight))
{
Assert.AreEqual(pointCount, CountPoints(c, minHeight, maxHeight));
}
if (errorCount != CountErrors(c, minHeight, maxHeight))
{
Assert.AreEqual(errorCount, CountErrors(c, minHeight, maxHeight));
}
return(true);
});
});
}
static GraphSummary FindGraph <TGraphPane>() where TGraphPane : SummaryGraphPane
{
GraphSummary result = null;
RunUI(() =>
{
foreach (var form in FormUtil.OpenForms.OfType <GraphSummary>())
{
TGraphPane graphPane;
if (form.TryGetGraphPane(out graphPane))
{
result = form;
break;
}
}
});
return(result);
}
private void VerifyGraphState(GraphSummary graphSummary, AreaGraphDisplayType displayType, int repCount, int pointCount, int errorCount = 0)
{
RunUI(() =>
{
Assert.AreEqual(repCount, graphSummary.CountCurves(c =>
{
if (pointCount != CountPoints(c))
{
Assert.AreEqual(pointCount, CountPoints(c));
}
if (errorCount != CountErrors(c))
{
Assert.AreEqual(errorCount, CountErrors(c));
}
return(displayType == AreaGraphDisplayType.bars
? c.IsBar
: c.IsLine);
}));
});
}
private void TestGraphSummary(GraphSummary active, GraphSummary[] others, bool shouldSync)
{
double min = 0.0;
double max = SkylineWindow.GraphChromatograms.Count();
double otherMin = -1.0;
double otherMax = 1.0;
RunUI(() =>
{
active.GraphControl.GraphPane.XAxis.Scale.Min = min;
active.GraphControl.GraphPane.XAxis.Scale.Max = max;
foreach (var graphSummary in others)
{
graphSummary.GraphControl.GraphPane.XAxis.Scale.Min = otherMin;
graphSummary.GraphControl.GraphPane.XAxis.Scale.Max = otherMax;
}
active.Activate();
SkylineWindow.SynchronizeSummaryZooming(active);
});
WaitForGraphs();
RunUI(() =>
{
double add = GetExpectedVisible(active) ? -1.0 : 0.0;
foreach (var graphSummary in others)
{
bool expectedVisible = GetExpectedVisible(graphSummary);
add += expectedVisible ? 1.0 : 0.0;
Assert.AreEqual(shouldSync ? min + add : otherMin, graphSummary.GraphControl.GraphPane.XAxis.Scale.Min);
Assert.AreEqual(shouldSync ? max + add : otherMax, graphSummary.GraphControl.GraphPane.XAxis.Scale.Max);
add += expectedVisible ? -1.0 : 0.0;
}
});
}
public HierarchicalClusterGraph()
{
InitializeComponent();
InitializeDendrograms();
var graphPane = zedGraphControl1.GraphPane;
graphPane.Title.IsVisible = false;
graphPane.XAxis.Title.IsVisible = false;
graphPane.YAxis.Title.IsVisible = false;
graphPane.Legend.IsVisible = false;
graphPane.Margin.All = 0;
graphPane.Border.IsVisible = false;
graphPane.XAxis.MinorTic.Size = 0;
graphPane.XAxis.MajorTic.IsOpposite = false;
graphPane.XAxis.MajorTic.Size = 2;
graphPane.YAxis.MinorTic.Size = 0;
graphPane.YAxis.MajorTic.IsOpposite = false;
graphPane.YAxis.MajorTic.Size = 2;
graphPane.X2Axis.MinorTic.Size = 0;
graphPane.X2Axis.MajorTic.Size = 0;
graphPane.Y2Axis.MinorTic.Size = 0;
graphPane.Y2Axis.MajorTic.Size = 0;
graphPane.XAxis.Scale.FontSpec = GraphSummary.CreateFontSpec(Color.Black);
graphPane.YAxis.Scale.FontSpec = GraphSummary.CreateFontSpec(Color.Black);
graphPane.YAxis.Scale.FontSpec.Angle = 90;
_xAxisLabelScaler = new AxisLabelScaler(graphPane, graphPane.XAxis)
{
IsRepeatRemovalAllowed = true
};
_yAxisLabelScaler = new AxisLabelScaler(graphPane, graphPane.YAxis)
{
IsRepeatRemovalAllowed = true
};
}
/// <summary>
/// Change the replicate "Order By" on a graph.
/// </summary>
/// <param name="graphSummary"></param>
/// <param name="menuItemPredicate">Function which returns true for the menu item that should be clicked.
/// The Document Order and Run Start Time items get chosen based on their position on the sub-menu.
/// The other items get chosen based on menu item text.</param>
private void OrderBy(GraphSummary graphSummary, Func <int, ToolStripMenuItem, bool> menuItemPredicate)
{
RunUI(() =>
{
graphSummary.GraphControl.ContextMenuStrip.Show(graphSummary.GraphControl, new Point(1, 1));
var orderByItem = SkylineWindow.ReplicateOrderContextMenuItem;
for (int index = 0; index < orderByItem.DropDownItems.Count; index++)
{
var item = orderByItem.DropDownItems[index] as ToolStripMenuItem;
if (item == null)
{
continue;
}
var predicate = menuItemPredicate(index, item);
if (predicate)
{
item.PerformClick();
return;
}
}
Assert.Fail();
});
}
public void UpdateGraphAndWait(GraphSummary graph)
{
RunUI(() => { graph.UpdateUI(); });
WaitForGraphs();
}
public RunToRunRegressionToolbar RegressionToolbar(GraphSummary graphSummary)
{
return(graphSummary.Toolbar as RunToRunRegressionToolbar);
}
public ToolStripComboBox RunToRunOriginalReplicate(GraphSummary graphSummary)
{
return(RegressionToolbar(graphSummary).RunToRunOriginalReplicate);
}
protected override void DoTest()
{
OpenDocument(TestFilesDir.GetTestPath(@"DIA-TTOF-tutorial.sky"));
WaitForDocumentLoaded();
RunUI(() => { SkylineWindow.ShowDetectionsReplicateComparisonGraph(); });
WaitForGraphs();
GraphSummary graph = SkylineWindow.DetectionsPlot;
var toolbar = graph.Toolbar as DetectionsToolbar;
Assert.IsNotNull(toolbar);
RunUI(() => { toolbar.CbLevel.SelectedItem = DetectionsGraphController.TargetType.PRECURSOR; });
WaitForGraphs();
DetectionsPlotPane pane;
Assert.IsTrue(graph.TryGetGraphPane(out pane));
Assert.IsTrue(pane.HasToolbar);
//use properties dialog to update the q-value
var propDialog = ShowDialog <DetectionToolbarProperties>(() =>
{
toolbar.pbProperties_Click(graph.GraphControl, new EventArgs());
});
//verify data correct for 2 q-values
RunUI(() =>
{
propDialog.SetQValueTo(0.003f);
propDialog.OkDialog();
});
WaitForClosedForm(propDialog);
WaitForCondition(() => (DetectionsGraphController.Settings.QValueCutoff == 0.003f));
AssertDataCorrect(pane, 0, 0.003f);
//use properties dialog to update the q-value
propDialog = ShowDialog <DetectionToolbarProperties>(() =>
{
toolbar.pbProperties_Click(graph.GraphControl, new EventArgs());
});
RunUI(() =>
{
propDialog.SetQValueTo(0.001f);
propDialog.OkDialog();
});
WaitForClosedForm(propDialog);
WaitForCondition(() => (DetectionsGraphController.Settings.QValueCutoff == 0.001f));
AssertDataCorrect(pane, 2, 0.001f);
//verify the number of the bars on the plot
RunUI(() =>
{
Assert.IsTrue(
pane.CurveList[0].IsBar && pane.CurveList[0].Points.Count == REF_DATA[0].Length);
});
string[] tipText =
{
Resources.DetectionPlotPane_Tooltip_Replicate + TextUtil.SEPARATOR_TSV_STR + @"2_SW-B",
string.Format(Resources.DetectionPlotPane_Tooltip_Count, DetectionsGraphController.TargetType.PRECURSOR) +
TextUtil.SEPARATOR_TSV_STR + 118.ToString(CultureInfo.CurrentCulture),
Resources.DetectionPlotPane_Tooltip_CumulativeCount + TextUtil.SEPARATOR_TSV_STR +
123.ToString(CultureInfo.CurrentCulture),
Resources.DetectionPlotPane_Tooltip_AllCount + TextUtil.SEPARATOR_TSV_STR +
115.ToString(CultureInfo.CurrentCulture),
Resources.DetectionPlotPane_Tooltip_QMedian + TextUtil.SEPARATOR_TSV_STR +
(6.0d).ToString(@"F1", CultureInfo.CurrentCulture)
};
RunUI(() =>
{
Assert.IsNotNull(pane.ToolTip);
pane.PopulateTooltip(1);
//verify the tooltip text
CollectionAssert.AreEqual(tipText, pane.ToolTip.TipLines);
});
//test the data correct after a doc change (delete peptide)
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 12);
SkylineWindow.EditDelete();
});
WaitForGraphs();
WaitForConditionUI(() => DetectionPlotData.GetDataCache().Datas.Any((dat) =>
ReferenceEquals(SkylineWindow.DocumentUI, dat.Document) &&
DetectionsGraphController.Settings.QValueCutoff == dat.QValueCutoff),
"Cache is not updated on document change.");
//verify that the cache is purged after the document update
RunUI(() =>
{
Assert.IsTrue(DetectionPlotData.GetDataCache().Datas.All((dat) =>
ReferenceEquals(SkylineWindow.DocumentUI, dat.Document)));
});
AssertDataCorrect(pane, 4, 0.001f);
RunUI(() => { SkylineWindow.ShowDetectionsHistogramGraph(); });
WaitForGraphs();
DetectionsHistogramPane paneHistogram;
var graphHistogram = SkylineWindow.DetectionsPlot;
Assert.IsTrue(graphHistogram.TryGetGraphPane(out paneHistogram), "Cannot get histogram pane.");
//display and hide tooltip
string[] histogramTipText =
{
Resources.DetectionHistogramPane_Tooltip_ReplicateCount + TextUtil.SEPARATOR_TSV_STR +
5.ToString(CultureInfo.CurrentCulture),
String.Format(Resources.DetectionHistogramPane_Tooltip_Count, DetectionsGraphController.TargetType.PRECURSOR) +
TextUtil.SEPARATOR_TSV_STR + 102.ToString(CultureInfo.CurrentCulture),
};
RunUI(() =>
{
Assert.IsNotNull(paneHistogram.ToolTip, "No tooltip found.");
paneHistogram.PopulateTooltip(5);
//verify the tooltip text
CollectionAssert.AreEqual(histogramTipText, paneHistogram.ToolTip.TipLines);
});
RunUI(() =>
{
graph.Close();
graphHistogram.Close();
});
WaitForGraphs();
}
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;
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);
}
}
public static PeptidesAndTransitionGroups GetSelectedPeptides(GraphSummary graphSummary)
{
return(PeptidesAndTransitionGroups.Get(graphSummary.StateProvider.SelectedNodes, graphSummary.ResultsIndex, int.MaxValue));
}
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 bool GetExpectedVisible(GraphSummary g)
{
var pane = g.GraphControl.GraphPane as AreaReplicateGraphPane;
return(pane != null && pane.IsExpectedVisible);
}