public void MakeFilesLists(ComparePeakBoundaries comparer, double falsePositiveCutoff, bool observed, out PointPairList filesPoints, out List <string> filesNames)
{
filesPoints = new PointPairList();
filesNames = new List <string>();
var matches = comparer.Matches;
var matchesByFile = matches.GroupBy(match => match.ReplicateName).OrderBy(group => group.Key);
int i = 1;
foreach (var matchGroup in matchesByFile)
{
PointPairList rocPoints;
var matchesInGroup = matchGroup.ToList();
if (comparer.HasNoScores)
{
matchesInGroup.Sort(PeakBoundsMatch.CompareQValue);
}
else
{
matchesInGroup.Sort(PeakBoundsMatch.CompareScore);
}
RocFromSortedMatches(matchesInGroup, Normalizer, out rocPoints);
var pointThreshold = GetCurveThreshold(rocPoints, falsePositiveCutoff, observed);
// Error is 2x the observed error rate, so that wiskers extend above and below bar item
// by the number of observed false-positives
filesPoints.Add(MeanErrorBarItem.MakePointPair(i++, pointThreshold.Y, pointThreshold.X * pointThreshold.Y * 2));
filesNames.Add(matchGroup.Key);
}
}
private void UpdateGraph()
{
if (!IsHandleCreated)
{
return;
}
zedGraphControl.GraphPane.GraphObjList.Clear();
zedGraphControl.GraphPane.CurveList.Clear();
_barGraph = null;
_rows = null;
var points = new PointPairList();
var groupComparisonModel = FoldChangeBindingSource.GroupComparisonModel;
var groupComparisonDef = groupComparisonModel.GroupComparisonDef;
var document = groupComparisonModel.Document;
var sequences = new List <Tuple <string, bool> >();
foreach (var nodePep in document.Molecules)
{
sequences.Add(new Tuple <string, bool>(nodePep.ModifiedTarget.DisplayName, nodePep.IsProteomic));
}
var uniquePrefixGenerator = new UniquePrefixGenerator(sequences, 3);
var textLabels = new List <string>();
var rows = _bindingListSource.OfType <RowItem>()
.Select(rowItem => rowItem.Value)
.OfType <FoldChangeBindingSource.FoldChangeRow>()
.ToArray();
bool showLabelType = rows.Select(row => row.IsotopeLabelType).Distinct().Count() > 1;
bool showMsLevel = rows.Select(row => row.MsLevel).Distinct().Count() > 1;
bool showGroup = rows.Select(row => row.Group).Distinct().Count() > 1;
foreach (var row in rows)
{
var foldChangeResult = row.FoldChangeResult;
double error = Math.Log(foldChangeResult.MaxFoldChange / foldChangeResult.FoldChange, 2.0);
var point = MeanErrorBarItem.MakePointPair(points.Count, foldChangeResult.Log2FoldChange, error);
points.Add(point);
string label;
if (null != row.Peptide)
{
try
{
label = uniquePrefixGenerator.GetUniquePrefix(
row.Peptide.GetDocNode().ModifiedTarget.DisplayName, row.Peptide.GetDocNode().IsProteomic);
}
catch
{
// Peptide must have been deleted.
label = row.Peptide.GetDocNode().ModifiedTarget.DisplayName;
}
}
else
{
label = ProteinMetadataManager.ProteinModalDisplayText(row.Protein.DocNode);
}
if (showMsLevel && row.MsLevel.HasValue)
{
label += @" MS" + row.MsLevel; //;
}
if (showLabelType && row.IsotopeLabelType != null)
{
label += @" (" + row.IsotopeLabelType.Title + @")";
}
if (showGroup && !Equals(row.Group, default(GroupIdentifier)))
{
label += @" " + row.Group;
}
textLabels.Add(label);
if (IsSelected(row))
{
double y, height;
if (foldChangeResult.Log2FoldChange >= 0)
{
y = foldChangeResult.Log2FoldChange + error;
height = y;
}
else
{
y = 0;
height = error - foldChangeResult.Log2FoldChange;
}
zedGraphControl.GraphPane.GraphObjList.Add(new BoxObj(point.X + .5, y, .99, height)
{
ZOrder = ZOrder.E_BehindCurves,
IsClippedToChartRect = true
});
}
}
zedGraphControl.GraphPane.XAxis.Title.Text = groupComparisonDef.PerProtein ? GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Protein : GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Peptide;
zedGraphControl.GraphPane.YAxis.Title.Text = GroupComparisonStrings.FoldChangeBarGraph_UpdateGraph_Log_2_Fold_Change;
var barGraph = new MeanErrorBarItem(null, points, Color.Black, Color.Blue);
zedGraphControl.GraphPane.CurveList.Add(barGraph);
zedGraphControl.GraphPane.XAxis.Scale.MinAuto = zedGraphControl.GraphPane.XAxis.Scale.MaxAuto =
zedGraphControl.GraphPane.YAxis.Scale.MinAuto = zedGraphControl.GraphPane.YAxis.Scale.MaxAuto = true;
zedGraphControl.GraphPane.XAxis.Type = AxisType.Text;
zedGraphControl.GraphPane.XAxis.Scale.TextLabels = textLabels.ToArray();
_axisLabelScaler.ScaleAxisLabels();
zedGraphControl.GraphPane.AxisChange();
zedGraphControl.Invalidate();
_barGraph = barGraph;
_rows = rows;
}
public void UpdateGraph()
{
var rocPane = zedGraphRoc.GraphPane;
var qqPane = zedGraphQq.GraphPane;
var filesPane = zedGraphFiles.GraphPane;
ClearGraphPane(rocPane);
ClearGraphPane(qqPane);
ClearGraphPane(filesPane);
if (!_peakBoundaryList.Any(comp => comp.IsActive))
{
InitializeGraphPanes();
return;
}
rocPane.Title.Text = Resources.ComparePeakPickingDlg_UpdateGraph_ROC_Plot_Comparison;
qqPane.Title.Text = Resources.ComparePeakPickingDlg_UpdateGraph_Q_Q_Comparison;
bool observed = checkObserved.Checked;
filesPane.Title.Text = string.Format(observed
? Resources.ComparePeakPickingDlg_UpdateGraph_Replicate_Comparison__Observed_FPR____0__
: Resources.ComparePeakPickingDlg_UpdateGraph_Replicate_Comparison__q_value____0__, textBoxFilesQCutoff.Text);
int i = -1;
const double minRocY = 0;
const double minRocX = 0;
double maxRocY = 0;
double maxRocX = 0;
double maxFilesY = 0;
double maxFilesX = 0;
double maxQq = 1e-6;
double minQq = 1;
var filesNames = new List <string>();
foreach (var comparer in _peakBoundaryList)
{
++i;
if (!comparer.IsActive)
{
continue;
}
PointPairList rocPoints;
MakeRocLists(comparer, Normalizer, out rocPoints);
maxRocY = Math.Max(maxRocY, rocPoints.Select(point => point.Y).Max());
maxRocX = _xAxisFocus ? X_AXIS_FOCUS : Math.Max(maxRocX, rocPoints.Select(point => point.X).Max());
var rocCurve = new LineItem(comparer.Name, rocPoints, _colors[i % _colors.Count], SymbolType.None, 3);
rocPane.CurveList.Add(rocCurve);
if (_showFpCutoff)
{
PlaceLabelAtCutoff(rocPoints, rocPane, Q_VALUE_SIG);
}
PointPairList filesPoints;
MakeFilesLists(comparer, _qValueSig, observed, out filesPoints, out filesNames);
maxFilesY = Math.Max(maxFilesY, filesPoints.Select(point => point.Y).Max());
maxFilesX = Math.Max(maxFilesX, filesPoints.Select(point => point.X).Max());
var bar = new MeanErrorBarItem(comparer.Name, filesPoints, _colors[i % _colors.Count], Color.Black);
bar.Bar.Fill.Type = FillType.Solid;
bar.Bar.Border.IsVisible = false;
filesPane.CurveList.Add(bar);
if (!comparer.HasNoQValues)
{
PointPairList qqPoints;
MakeQValueLists(comparer, out qqPoints);
double maxQqPoint = qqPoints.Select(point => Math.Max(point.X, point.Y)).Max();
var qqNonzeros = qqPoints.Where(point => point.Y > 0).Select(point => point.Y).ToList();
double minQqYPoint = qqNonzeros.Any() ? qqNonzeros.Min() : 0.001;
maxQq = Math.Max(maxQq, maxQqPoint);
minQq = Math.Min(minQq, minQqYPoint);
var qqCurve = new LineItem(comparer.Name, qqPoints, _colors[i % _colors.Count], SymbolType.None, 3);
qqPane.CurveList.Add(qqCurve);
if (_showFpCutoffQ)
{
PlaceLabelAtCutoff(qqPoints, qqPane, Q_VALUE_SIG);
}
}
}
var minQqPlot = Math.Min(minQq * MIN_SIG_FP, Q_VALUE_SIG * 0.5);
var maxQqPlot = Math.Max(maxQq * MARGIN, Q_VALUE_SIG * MARGIN);
var equalityPoints = new PointPairList {
{ minQqPlot, minQqPlot }, { 1, 1 }
};
var equalityCurve = new LineItem(Resources.ComparePeakPickingDlg_UpdateGraph_Equality, equalityPoints, Color.Black, SymbolType.None);
qqPane.CurveList.Add(equalityCurve);
if (_showFpCutoffQ)
{
var significancePoints = new PointPairList {
{ Q_VALUE_SIG, minQq }, { Q_VALUE_SIG, maxQq }
};
var significanceCurve = new LineItem(string.Format(Resources.ComparePeakPickingDlg_UpdateGraph__0__significance_threshold, Q_VALUE_SIG), significancePoints, _colorSigLine, SymbolType.None);
qqPane.CurveList.Add(significanceCurve);
}
if (_showFpCutoff)
{
var significancePointsRoc = new PointPairList {
{ Q_VALUE_SIG, minRocY }, { Q_VALUE_SIG, maxRocY *MARGIN }
};
var significanceCurveRoc = new LineItem(string.Format(Resources.ComparePeakPickingDlg_UpdateGraph__0__observed_false_positive_rate, Q_VALUE_SIG), significancePointsRoc, _colorSigLine, SymbolType.None);
rocPane.CurveList.Add(significanceCurveRoc);
}
rocPane.XAxis.Scale.Min = minRocX;
rocPane.XAxis.Scale.Max = maxRocX * MARGIN;
rocPane.YAxis.Scale.Min = minRocY;
rocPane.YAxis.Scale.Max = maxRocY * MARGIN;
qqPane.XAxis.Scale.Min = minQqPlot;
qqPane.XAxis.Scale.Max = maxQqPlot;
qqPane.YAxis.Scale.Min = minQqPlot;
qqPane.YAxis.Scale.Max = maxQqPlot;
qqPane.XAxis.Type = AxisType.Log;
qqPane.YAxis.Type = AxisType.Log;
filesPane.XAxis.Scale.Min = 0;
filesPane.XAxis.Scale.Max = maxFilesX + 1;
filesPane.YAxis.Scale.Min = 0;
filesPane.YAxis.Scale.Max = maxFilesY * MARGIN;
zedGraphRoc.AxisChange();
zedGraphRoc.Refresh();
zedGraphQq.AxisChange();
zedGraphQq.Refresh();
zedGraphFiles.AxisChange();
zedGraphFiles.Refresh();
filesPane.XAxis.Scale.TextLabels = filesNames.ToArray();
filesPane.XAxis.Type = AxisType.Text;
_axisLabelScaler.ScaleAxisLabels();
}
