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;
//draw bars
var countPoints = new PointPairList(Enumerable.Range(0, _detectionData.ReplicateCount)
.Select(i => new PointPair(i, TargetData.Histogram[i] / YScale)).ToList());
CurveList.Insert(0, MakeBarItem(countPoints, Color.FromArgb(180, 220, 255)));
//axes formatting
XAxis.Scale.Max = _detectionData.ReplicateCount + 1;
YAxis.Scale.Max = TargetData.Histogram.Max() / YScale * 1.15;
}
public void moveBarsToBack()
{
CurveList.Move(0, 999);
var points = new PointPairList();
Objects.each(Objects.sort(dateParent.dates()), time => points.Add(new XDate(time).XLDate, 0.0));
var line = new LineItem("", points, Color.Black, SymbolType.None)
{
Line = { IsVisible = false },
Symbol = { IsVisible = false },
Label = { IsVisible = false }
};
CurveList.Insert(0, line);
}
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;
_percentage = !Settings.Default.AreaCVShowDecimals;
_decimals = _percentage ? 1 : 3;
CurveList.Clear();
var gotData = _cache.TryGet(_document, settings, DataCallback, out _areaCVGraphData);
if (!gotData)
{
Title.Text = Resources.AreaCVHistogram2DGraphPane_UpdateGraph_Calculating____;
return;
}
if (!_areaCVGraphData.IsValid)
{
Title.Text = Resources.AreaCVHistogram2DGraphPane_Draw_Not_enough_data;
return;
}
var factor = AreaGraphController.GetAreaCVFactorToDecimal();
Title.Text = string.Empty;
YAxis.Title.Text = Resources.AreaCVHistogram2DGraphPane_UpdateGraph_CV + (_percentage ? @" (%)" : string.Empty);
XAxis.Title.Text = Resources.AreaCvHistogram2DGraphPane_UpdateGraph_Log10_Mean_Area;
XAxis.Scale.MinAuto = XAxis.Scale.MinAuto = XAxis.Scale.MaxAuto = YAxis.Scale.MaxAuto = false;
XAxis.Scale.Min = Math.Max(0, double.IsNaN(Settings.Default.AreaCVMinLog10Area) ? _areaCVGraphData.MinMeanArea : Settings.Default.AreaCVMinLog10Area);
XAxis.Scale.Max = double.IsNaN(Settings.Default.AreaCVMaxLog10Area) ? _areaCVGraphData.MaxMeanArea : Settings.Default.AreaCVMaxLog10Area;
YAxis.Scale.Min = 0.0;
YAxis.Scale.Max = double.IsNaN(Settings.Default.AreaCVMaxCV) ? _areaCVGraphData.MaxCV * factor : Settings.Default.AreaCVMaxCV;
AxisChange();
var points = _areaCVGraphData.Data
.Select(d => new HeatMapData.TaggedPoint3D(new Point3D(d.MeanArea, d.CV * factor, d.Frequency), d))
.ToList();
Items = points.Count; // Because heatmaps can't be trusted to have a consistent number of points on all monitors
var heatMapData = new HeatMapData(points);
HeatMapGraphPane.GraphHeatMap(this, heatMapData, 17, 2, (float)(_areaCVGraphData.MinCV * factor), (float)(_areaCVGraphData.MaxCV * factor), Settings.Default.AreaCVLogScale, 0);
var unit = _percentage ? @"%" : string.Empty;
if (Settings.Default.AreaCVShowMedianCV)
{
string text = string.Format(Resources.AreaCVHistogram2DGraphPane_UpdateGraph_Median___0_, HistogramHelper.FormatDouble(_areaCVGraphData.MedianCV * factor, _decimals) + unit);
_lineItems[0] = AddLineItem(text, XAxis.Scale.Min, XAxis.Scale.Max, _areaCVGraphData.MedianCV * factor, _areaCVGraphData.MedianCV * factor, Color.Blue);
CurveList.Insert(0, _lineItems[0]);
}
if (Settings.Default.AreaCVShowCVCutoff)
{
string text = string.Format(Resources.AreaCVHistogramGraphPane_UpdateGraph_Below__0____1_, Settings.Default.AreaCVCVCutoff + unit,
HistogramHelper.FormatDouble(_areaCVGraphData.BelowCVCutoff * factor, _decimals) +
unit);
_lineItems[1] = AddLineItem(text, XAxis.Scale.Min, XAxis.Scale.Max, Settings.Default.AreaCVCVCutoff, Settings.Default.AreaCVCVCutoff, Color.Red);
CurveList.Insert(0, _lineItems[1]);
}
}
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),
});
}
}
public override void SetScale(Graphics g)
{
if (!ShowHeatMap || _heatMapData == null)
{
base.SetScale(g);
return;
}
CurveList.Clear();
XAxis.Scale.SetupScaleData(this, XAxis);
YAxis.Scale.SetupScaleData(this, YAxis);
double cellWidth = Math.Abs(XAxis.Scale.ReverseTransform(MinDotRadius) - XAxis.Scale.ReverseTransform(0));
double cellHeight = Math.Abs(YAxis.Scale.ReverseTransform(MinDotRadius) - YAxis.Scale.ReverseTransform(0));
if (cellWidth <= 0 || double.IsNaN(cellWidth) || cellHeight <= 0 || double.IsNaN(cellHeight))
{
return;
}
// Use log scale for heat intensity.
double scale = (_heatMapColors.Length - 1) / Math.Log(_heatMapData.MaxPoint.Z);
// Create curves for each intensity color.
var curves = new LineItem[_heatMapColors.Length];
for (int i = 0; i < curves.Length; i++)
{
var color = _heatMapColors[i];
curves[i] = new LineItem(string.Empty)
{
Line = new Line {
IsVisible = false
},
Symbol = new Symbol
{
Border = new Border {
IsVisible = false
},
Size = (int)(MinDotRadius + i / (double)(curves.Length - 1) * (MaxDotRadius - MinDotRadius)),
Fill = new Fill(color),
Type = SymbolType.Circle,
IsAntiAlias = true
}
};
if ((i + 1) % (_heatMapColors.Length / 4) == 0)
{
double intensity = Math.Pow(Math.E, i / scale);
curves[i].Label.Text = intensity.ToString("F0"); // Not L10N
}
CurveList.Insert(0, curves[i]);
}
// Get points within bounds of graph/filter, with density appropriate for the current display resolution.
var points = _heatMapData.GetPoints(
XAxis.Scale.Min,
XAxis.Scale.Max,
Math.Max(YAxis.Scale.Min, _yMin),
Math.Min(YAxis.Scale.Max, _yMax),
cellWidth,
cellHeight);
foreach (var heatPoint in points)
{
// A log scale produces a better visual display.
int intensity = (int)(Math.Log(heatPoint.Z) * scale);
if (intensity >= 0)
{
curves[intensity].AddPoint(heatPoint.X, heatPoint.Y);
}
}
}
