private void zedGraphControl_ContextMenuBuilder(ZedGraphControl sender, ContextMenuStrip menuStrip, Point mousePt, ZedGraphControl.ContextMenuObjectState objState)
{
int?replicateIndexFromPoint = ReplicateIndexFromPoint(mousePt);
if (replicateIndexFromPoint.HasValue)
{
ToolStripMenuItem excludeStandardMenuItem = MakeExcludeStandardMenuItem(replicateIndexFromPoint.Value);
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));
}
logPlotContextMenuItem.Checked = Options.LogPlot;
showLegendContextMenuItem.Checked = Options.ShowLegend;
showSelectionContextMenuItem.Checked = Options.ShowSelection;
ZedGraphHelper.BuildContextMenu(sender, menuStrip, true);
if (!menuStrip.Items.Contains(logPlotContextMenuItem))
{
int index = 0;
menuStrip.Items.Insert(index++, logPlotContextMenuItem);
menuStrip.Items.Insert(index++, showSampleTypesContextMenuItem);
menuStrip.Items.Insert(index++, showLegendContextMenuItem);
menuStrip.Items.Insert(index++, showSelectionContextMenuItem);
menuStrip.Items.Insert(index++, new ToolStripSeparator());
}
}
public void SetDisplaySampleType(SampleType sampleType, bool display)
{
if (display)
{
DisplaySampleTypes = DisplaySampleTypes.Concat(new[] {sampleType.Name}).Distinct().ToArray();
}
else
{
DisplaySampleTypes = DisplaySampleTypes.Except(new[] {sampleType.Name}).ToArray();
}
}
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 ToolStripMenuItem MakeShowSampleTypeMenuItem(SampleType sampleType)
{
ToolStripMenuItem menuItem = new ToolStripMenuItem(sampleType.ToString())
{
Checked = Options.DisplaySampleTypes.Contains(sampleType.Name)
};
menuItem.Click += (sender, args) =>
{
if (menuItem.Checked)
{
Options.DisplaySampleTypes = Options.DisplaySampleTypes.Except(new[] {sampleType.Name}).ToArray();
}
else
{
Options.DisplaySampleTypes =
Options.DisplaySampleTypes.Concat(new[] {sampleType.Name}).Distinct().ToArray();
}
UpdateUI(false);
};
return menuItem;
}
private void zedGraphControl_ContextMenuBuilder(ZedGraphControl sender, ContextMenuStrip menuStrip, Point mousePt, ZedGraphControl.ContextMenuObjectState objState)
{
ZedGraphHelper.BuildContextMenu(sender, menuStrip, true);
if (!menuStrip.Items.Contains(logPlotContextMenuItem))
{
int index = 0;
menuStrip.Items.Insert(index++, logPlotContextMenuItem);
menuStrip.Items.Insert(index++, showSampleTypesContextMenuItem);
menuStrip.Items.Insert(index++, showLegendContextMenuItem);
menuStrip.Items.Insert(index++, showSelectionContextMenuItem);
menuStrip.Items.Insert(index++, new ToolStripSeparator());
}
showSampleTypesContextMenuItem.DropDownItems.Clear();
foreach (var sampleType in SampleType.ListSampleTypes())
{
showSampleTypesContextMenuItem.DropDownItems.Add(MakeShowSampleTypeMenuItem(sampleType));
}
logPlotContextMenuItem.Checked = Options.LogPlot;
showLegendContextMenuItem.Checked = Options.ShowLegend;
showSelectionContextMenuItem.Checked = Options.ShowSelection;
}
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 bool Equals(SampleType other)
{
return Name.Equals(other.Name);
}
public bool DisplaySampleType(SampleType sampleType)
{
return(DisplaySampleTypes.Contains(sampleType.Name));
}
public bool DisplaySampleType(SampleType sampleType)
{
return DisplaySampleTypes.Contains(sampleType.Name);
}
public ChromatogramSet ChangeSampleType(SampleType sampleType)
{
return ChangeProp(ImClone(this), im => im.SampleType = sampleType ?? SampleType.DEFAULT);
}
private bool Equals(SampleType other)
{
return(Name.Equals(other.Name));
}
private ToolStripMenuItem MakeShowSampleTypeMenuItem(SampleType sampleType)
{
ToolStripMenuItem menuItem = new ToolStripMenuItem(sampleType.ToString())
{
Checked = Options.DisplaySampleTypes.Contains(sampleType.Name)
};
menuItem.Click += (sender, args) =>
{
if (menuItem.Checked)
{
Options.DisplaySampleTypes = Options.DisplaySampleTypes.Except(new[] {sampleType.Name}).ToArray();
}
else
{
Options.DisplaySampleTypes =
Options.DisplaySampleTypes.Concat(new[] {sampleType.Name}).Distinct().ToArray();
}
UpdateUI(false);
};
return menuItem;
}
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);
}
}