private TextObj AddLabel(string text, double x, double y, Color color)
{
return(new TextObj(text, x, y, CoordType.AxisXYScale, AlignH.Center, AlignV.Bottom)
{
FontSpec = GraphSummary.CreateFontSpec(color),
IsClippedToChartRect = true
});
}
public override void Draw(Graphics g)
{
GraphObjList.Clear();
if (_graphData != null)
{
// Force Axes to recalculate to ensure proper layout of labels
AxisChange(g);
// Reposition the regression label.
RectangleF rectChart = Chart.Rect;
PointF ptTop = rectChart.Location;
// Setup axes scales to enable the ReverseTransform method
XAxis.Scale.SetupScaleData(this, XAxis);
YAxis.Scale.SetupScaleData(this, YAxis);
float yNext = ptTop.Y;
double left = XAxis.Scale.ReverseTransform(ptTop.X + 8);
FontSpec fontSpec = GraphSummary.CreateFontSpec(COLOR_LINE_REGRESSION);
if (_labelRegression != null)
{
// Add regression text
double top = YAxis.Scale.ReverseTransform(yNext);
TextObj text = new TextObj(_labelRegression, left, top,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = fontSpec,
};
// text.FontSpec.Size = 12;
GraphObjList.Add(text);
}
if (_labelRegressionCurrent != null)
{
// Add text for current regression
SizeF sizeLabel = fontSpec.MeasureString(g, _labelRegression, CalcScaleFactor());
yNext += sizeLabel.Height + 3;
double top = YAxis.Scale.ReverseTransform(yNext);
TextObj text = new TextObj(_labelRegressionCurrent, left, top,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(COLOR_LINE_REGRESSION_CURRENT),
};
// text.FontSpec.Size = 12;
GraphObjList.Add(text);
}
}
base.Draw(g);
}
private void AddLabels(Graphics g)
{
if (_areaCVGraphData == null)
{
Title.Text = Resources.AreaCVHistogramGraphPane_AddLabels_Calculating____;
}
else if (!_areaCVGraphData.IsValid)
{
Title.Text = Resources.AreaCVHistogramGraphPane_AddLabels_Not_enough_data;
}
else
{
Title.Text = string.Empty;
var unit = _percentage ? @"%" : string.Empty;
var factor = _percentage ? 100.0 : 1.0;
var scaleFactor = CalcScaleFactor();
var fontHeight = GraphSummary.CreateFontSpec(Color.Black).GetHeight(scaleFactor);
var height = PaneHeightToYValue(fontHeight);
// Anchor labels at top of graph pane
var y = Math.Min(PaneHeightToYValue(Rect.Height - TitleGap * Title.FontSpec.GetHeight(scaleFactor) - fontHeight * _stickItems.Count), _areaCVGraphData.MaxFrequency + height);
var index = 0;
if (Settings.Default.AreaCVShowMedianCV)
{
_stickItems[index++].Points[1].Y = y;
string text = string.Format(Resources.AreaCVHistogramGraphPane_AddLabels_Median___0_,
HistogramHelper.FormatDouble(_areaCVGraphData.MedianCV * factor, _decimals) + unit);
GraphObjList.Add(AddLabel(text, _areaCVGraphData.MedianCV * factor, y, Color.Blue));
y += height;
}
if (Settings.Default.AreaCVShowCVCutoff)
{
_stickItems[index++].Points[1].Y = y;
string text = string.Format(Resources.AreaCVHistogramGraphPane_UpdateGraph_Below__0____1_,
Settings.Default.AreaCVCVCutoff + unit, HistogramHelper.FormatDouble(_areaCVGraphData.BelowCVCutoff * factor, _decimals) + unit);
GraphObjList.Add(AddLabel(text, Settings.Default.AreaCVCVCutoff, y, Color.Red));
}
}
}
private static float AddRegressionLabel(PaneBase graphPane, Graphics g, double score, double time,
RetentionTimeRegression regression, RetentionTimeStatistics statistics, Color color)
{
string label;
if (regression == null || regression.Conversion == null || statistics == null)
{
label = String.Format("{0} = ?, {1} = ?\n" + "{2} = ?\n" + "r = ?", // Not L10N
Resources.Regression_slope,
Resources.Regression_intercept,
Resources.GraphData_AddRegressionLabel_window);
}
else
{
label = String.Format("{0} = {1:F02}, {2} = {3:F02}\n" + "{4} = {5:F01}\n" + "r = {6}", // Not L10N
Resources.Regression_slope,
regression.Conversion.Slope,
Resources.Regression_intercept,
regression.Conversion.Intercept,
Resources.GraphData_AddRegressionLabel_window,
regression.TimeWindow,
Math.Round(statistics.R, RetentionTimeRegression.ThresholdPrecision));
}
TextObj text = new TextObj(label, score, time,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(color),
};
graphPane.GraphObjList.Add(text);
// Measure the text just added, and return its height
SizeF sizeLabel = text.FontSpec.MeasureString(g, label, graphPane.CalcScaleFactor());
return(sizeLabel.Height + 3);
}
public void AddLabels(GraphPane graphPane, Graphics g)
{
if (_bins.Length == 0)
{
graphPane.Title.Text = Resources.MassErrorHistogramGraphPane_AddLabels_Mass_Errors_Unavailable;
return;
}
graphPane.Title.Text = String.Empty;
var rectChart = graphPane.Chart.Rect;
var ptTop = rectChart.Location;
// Setup axes scales to enable the ReverseTransform method
var xAxis = graphPane.XAxis;
xAxis.Scale.SetupScaleData(graphPane, xAxis);
var yAxis = graphPane.YAxis;
yAxis.Scale.SetupScaleData(graphPane, yAxis);
var yNext = ptTop.Y;
var scoreLeft = xAxis.Scale.ReverseTransform(ptTop.X + 8);
var timeTop = yAxis.Scale.ReverseTransform(yNext);
// ReSharper disable LocalizableElement
var label = string.Format("{0} = {1:F01},\n" + "{2} = {3:F01}\n",
// ReSharper restore LocalizableElement
Resources.MassErrorHistogramGraphPane_AddLabels_mean, _mean,
Resources.MassErrorHistogramGraphPane_AddLabels_standard_deviation, _stdDev);
var text = new TextObj(label, scoreLeft, timeTop, CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black)
};
graphPane.GraphObjList.Add(text);
}
public override void AddAnnotations(MSGraphPane graphPane, Graphics g, MSPointList pointList, GraphObjList annotations)
{
// ReSharper disable UseObjectOrCollectionInitializer
foreach (var rmi in SpectrumInfo.PeaksMatched)
{
if (!IsVisibleIon(rmi))
{
continue;
}
var matchedIon = rmi.MatchedIons.First(IsVisibleIon);
Color color;
switch (matchedIon.IonType)
{
default: color = COLOR_NONE; break;
case IonType.a: color = COLOR_A; break;
case IonType.x: color = COLOR_X; break;
case IonType.b: color = COLOR_B; break;
case IonType.y: color = COLOR_Y; break;
case IonType.c: color = COLOR_C; break;
case IonType.z: color = COLOR_Z; break;
case IonType.custom: color = (rmi.Rank > 0) ? COLOR_OTHER_IONS : COLOR_NONE; break; // Small molecule fragments - only color if ranked
case IonType.precursor: color = COLOR_PRECURSOR; break;
}
if (Invert)
{
color = InvertColor(color);
}
if (rmi.MatchedIons.Any(mfi => IsMatch(mfi.PredictedMz)))
{
color = COLOR_SELECTED;
}
double mz = rmi.ObservedMz;
var intensity = Invert ? -rmi.Intensity : rmi.Intensity;
var stick = new LineObj(color, mz, intensity, mz, 0);
stick.IsClippedToChartRect = true;
stick.Location.CoordinateFrame = CoordType.AxisXYScale;
stick.Line.Width = LineWidth + 1;
annotations.Add(stick);
}
//ReSharper restore UseObjectOrCollectionInitializer
if (ShowScores && SpectrumInfo.Score.HasValue)
{
var text = new TextObj(
string.Format(LocalizationHelper.CurrentCulture, Resources.AbstractSpectrumGraphItem_AddAnnotations_, SpectrumInfo.Score),
0.01, 0, CoordType.ChartFraction, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
};
annotations.Add(text);
}
}
public override void UpdateGraph(bool selectionChanged)
{
if (!GraphSummary.DocumentUIContainer.DocumentUI.Settings.HasResults)
{
_areaCVGraphData = null;
return;
}
var settings = new AreaCVGraphData.AreaCVGraphSettings(GraphSummary.Type);
_document = GraphSummary.DocumentUIContainer.DocumentUI;
var factor = AreaGraphController.GetAreaCVFactorToDecimal();
BarSettings.Type = BarType.SortedOverlay;
BarSettings.ClusterScaleWidth = Settings.Default.AreaCVHistogramBinWidth;
BarSettings.MinClusterGap = 0.0f;
_percentage = !Settings.Default.AreaCVShowDecimals;
_decimals = _percentage ? 1 : 3;
GraphObjList.Clear();
CurveList.Clear();
_stickItems.Clear();
var gotData = _cache.TryGet(_document, settings, DataCallback, out _areaCVGraphData);
if (!gotData || !_areaCVGraphData.IsValid)
{
return;
}
var fontHeight = GraphSummary.CreateFontSpec(Color.Black).GetHeight(CalcScaleFactor());
var height = PaneHeightToYValue(fontHeight);
var heightFactor = 1;
if (Settings.Default.AreaCVShowMedianCV)
{
var stick = AddStickItem(_areaCVGraphData.MedianCV * factor, _areaCVGraphData.MedianCV * factor, 0.0, _areaCVGraphData.MaxFrequency + heightFactor++ *height, Color.Blue);
CurveList.Add(stick);
_stickItems.Add(stick);
}
if (Settings.Default.AreaCVShowCVCutoff)
{
var stick = AddStickItem(Settings.Default.AreaCVCVCutoff, Settings.Default.AreaCVCVCutoff, 0.0, _areaCVGraphData.MaxFrequency + heightFactor++ *height, Color.Red);
CurveList.Add(stick);
_stickItems.Add(stick);
}
var selected = HistogramHelper.GetSelectedPeptides(GraphSummary).NodePeps.OrderBy(p => p.Id.GlobalIndex).ToList();
var comparer = Comparer <PeptideDocNode> .Create((a, b) => a.Id.GlobalIndex.CompareTo(b.Id.GlobalIndex));
var selectedPoints = new PointPairList();
var selectedPoints2 = new PointPairList();
var otherPoints = new PointPairList();
foreach (var d in _areaCVGraphData.Data)
{
int frequency;
var x = d.CV * factor + Settings.Default.AreaCVHistogramBinWidth / 2.0f;
var pt = new PointPair(x, d.Frequency)
{
Tag = d
};
if (Settings.Default.ShowReplicateSelection &&
(frequency = d.PeptideAnnotationPairs.Count(pair => selected.BinarySearch(pair.Peptide, comparer) >= 0)) > 0)
{
selectedPoints.Add(pt);
selectedPoints2.Add(new PointPair(x, frequency)
{
Tag = d
});
}
else
{
otherPoints.Add(pt);
}
}
CurveList.Insert(0, MakeBarItem(selectedPoints2, Color.Red));
CurveList.Insert(1, MakeBarItem(selectedPoints, Color.FromArgb(Color.Red.ToArgb() & 0x7FFFFFFF)));
CurveList.Insert(2, MakeBarItem(otherPoints, Color.FromArgb(180, 220, 255)));
XAxis.Title.Text = Resources.AreaCVHistogramGraphPane_UpdateGraph_CV + (_percentage ? @" (%)" : string.Empty);
YAxis.Title.Text = Resources.AreaCVHistogramGraphPane_UpdateGraph_Frequency;
XAxis.Scale.Min = YAxis.Scale.Min = 0;
XAxis.Scale.MinAuto = XAxis.Scale.MaxAuto = YAxis.Scale.MinAuto = YAxis.Scale.MaxAuto = false;
if (!double.IsNaN(Settings.Default.AreaCVMaxCV))
{
XAxis.Scale.Max = Settings.Default.AreaCVMaxCV;
}
else
{
XAxis.Scale.Max = _areaCVGraphData.MaxCV * factor + Settings.Default.AreaCVHistogramBinWidth;
}
if (!double.IsNaN(Settings.Default.AreaCVMaxFrequency))
{
YAxis.Scale.Max = Settings.Default.AreaCVMaxFrequency;
}
else
{
YAxis.Scale.Max = _areaCVGraphData.MaxFrequency + heightFactor * height;
}
AxisChange();
}
public override void UpdateGraph(bool selectionChanged)
{
GraphObjList.Clear();
CurveList.Clear();
Legend.IsVisible = false;
if (!DetectionPlotData.GetDataCache().TryGet(
GraphSummary.DocumentUIContainer.DocumentUI, Settings.QValueCutoff, this.DataCallback,
out _detectionData))
{
return;
}
AddLabels();
BarSettings.Type = BarType.SortedOverlay;
BarSettings.MinClusterGap = 0.3f;
Legend.IsVisible = Settings.ShowLegend;
var emptySymbol = new Symbol(SymbolType.None, Color.Transparent);
//draw bars
var counts = TargetData.TargetsCount;
var countPoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, counts[i] / YScale)).ToList());
CurveList.Insert(0, MakeBarItem(countPoints, Color.FromArgb(180, 220, 255)));
//draw cumulative curve
counts = TargetData.TargetsCumulative;
var cumulativePoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, counts[i] / YScale)).ToList());
CurveList.Insert(1,
new LineItem(Resources.DetectionPlotPane_CumulativeLine_Name)
{
Points = cumulativePoints,
Symbol = emptySymbol,
Line = new Line()
{
Color = Color.Coral, Width = 2
}
});
//draw inclusive curve
counts = TargetData.TargetsAll;
var allPoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, counts[i] / YScale)).ToList());
CurveList.Insert(2,
new LineItem(Resources.DetectionPlotPane_AllRunsLine_Name)
{
Symbol = emptySymbol,
Points = allPoints,
Line = new Line()
{
Color = Color.Black, Width = 2
}
});
//axes formatting
XAxis.Scale.Max = _detectionData.ReplicateCount + 1;
YAxis.Scale.Max = _detectionData.GetTargetData(Settings.TargetType).MaxCount / YScale * 1.15;
if (Settings.ShowAtLeastN)
{
double lineY = TargetData.getCountForMinReplicates(Settings.RepCount);
var atLeastLine = new Line()
{
Width = 1, Color = Color.Blue, Style = DashStyle.Dash
};
var dummyPoints = new PointPairList(new[] { new PointPair(0, 0) });
var line = new LineObj(Color.Blue, 0, lineY / YScale, XAxis.Scale.Max, lineY / YScale)
{
IsClippedToChartRect = true,
Line = atLeastLine
};
GraphObjList.Add(line);
//This is a placeholder to make sure the line shows in the legend.
CurveList.Insert(3,
new LineItem(String.Format(CultureInfo.CurrentCulture,
Resources.DetectionPlotPane_AtLeastLine_Name,
Settings.RepCount, _detectionData.ReplicateCount, lineY))
{
Symbol = emptySymbol,
Points = dummyPoints,
Line = atLeastLine
});
}
if (Settings.ShowSelection)
{
var selectedIndex = GraphSummary.StateProvider.SelectedResultsIndex;
var lineLength = TargetData.TargetsCount[selectedIndex] / YScale + YAxis.Scale.Max * 0.05;
GraphObjList.Add(
new LineObj(Color.Black, selectedIndex + 1, 0, selectedIndex + 1, lineLength)
{
IsClippedToChartRect = true,
Line = new Line()
{
Width = 1, Color = Color.Black, Style = DashStyle.Dash
}
});
}
if (Settings.ShowMean)
{
var stats = new Statistics(TargetData.TargetsCount.Select((x) => (double)x));
var labelText = String.Format(CultureInfo.CurrentCulture,
TextUtil.LineSeparate(new[]
{
Resources.DetectionPlotPane_Label_Mean,
Resources.DetectionPlotPane_Label_Stddev
}
),
stats.Mean(), stats.StdDev());
GraphObjList.Add(new TextObj(labelText, 0.1, YAxis.Scale.Max,
CoordType.AxisXYScale, AlignH.Left, AlignV.Top)
{
IsClippedToChartRect = true,
ZOrder = ZOrder.E_BehindCurves,
FontSpec = GraphSummary.CreateFontSpec(Color.Black),
});
}
}
