private void dataGridViewIDs_CellClick(object sender, DataGridViewCellEventArgs e)
{
try
{
string loccus = dataGridViewIDs.Rows[e.RowIndex].Cells[0].Value.ToString();
Console.WriteLine(e.RowIndex.ToString() + " clicked. Locus: " + loccus);
AnovaItem ai = anovaResults.Find(a => a.Locus.Equals(loccus));
chartAnova.Series.Clear();
double maxY = double.NegativeInfinity;
richTextBoxDataPoints.Clear();
foreach (Series s in ai.MyChart.Series)
{
richTextBoxDataPoints.Text += s.Name + "\n";
chartAnova.Series.Add(new Series(s.Name));
foreach (DataPoint p in s.Points)
{
chartAnova.Series.Last().Points.Add(p);
richTextBoxDataPoints.Text += p.YValues[0] + "\t";
if (p.YValues[0] > maxY)
{
maxY = p.YValues[0];
}
}
richTextBoxDataPoints.Text += "\n";
}
chartAnova.Titles[0].Text = loccus;
chartAnova.ChartAreas[0].AxisY.Maximum = maxY * 1.1;
chartAnova.ChartAreas[0].AxisY.Title = "Signal";
chartAnova.ChartAreas[0].AxisX.Title = "Replicate ID";
this.Update();
}
catch
{
Console.WriteLine("Unable to retrieve locus information");
}
}
private void Populate()
{
List <AnovaItem> AnovaResults = new List <AnovaItem>();
List <int> allClasses = plp.MySparseMatrix.ExtractLabels();
if (plp.MySparseMatrix.ClassDescriptionDictionary.Keys.Count == 0)
{
//There is no class description dictionary so we will create one
foreach (int c in allClasses)
{
plp.MySparseMatrix.ClassDescriptionDictionary.Add(c, c.ToString());
}
}
anovaResults = new List <AnovaItem>(plp.MyIndex.TheIndexes.Count);
List <double> allQuantitationValues = new List <double>();
foreach (PatternTools.SparseMatrixIndexParserV2.Index i in plp.MyIndex.TheIndexes)
{
Console.WriteLine(i.ID + "\t" + i.Name);
Dictionary <int, List <double> > valueDict = new Dictionary <int, List <double> >();
List <int> noItems = new List <int>();
foreach (var kvp in plp.MySparseMatrix.ClassDescriptionDictionary)
{
List <double> values = plp.MySparseMatrix.ExtractDimValues(i.ID, kvp.Key, false);
allQuantitationValues.AddRange(values);
noItems.Add(values.Count);
valueDict.Add(kvp.Key, values);
}
double sum = 0;
foreach (KeyValuePair <int, List <double> > kvp in valueDict)
{
sum += valueDict.Count;
}
if (sum == 0)
{
continue;
}
//We will only consider cases of which we have the same number of readings for each class
if (noItems.Distinct().Count() == 1 && !noItems.Contains(1))
{
if (noItems[0] == 0)
{
Console.WriteLine("A protein with 0 quantitation for all three conditions was found");
continue;
}
AnovaItem a = new AnovaItem(i.Name, i.ID, i.Description, valueDict, plp.MySparseMatrix.ClassDescriptionDictionary, (double)numericUpDownQValue.Value);
if (!double.IsInfinity(a.MyAnovaResult.FRatio))
{
try
{
double p = 1 - alglib.fdistr.fdistribution((int)a.MyAnovaResult.DegreeOfFreedomBetweenGroups, (int)a.MyAnovaResult.DegreeOfFreedomWithinGroups, a.MyAnovaResult.FRatio);
Console.WriteLine(p);
anovaResults.Add(a);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
}
}
}
}
chartHistogram.Series[0].Points.Clear();
List <PatternTools.HistogramHelper.HistogramBin> hBins = PatternTools.HistogramHelper.BinData(allQuantitationValues, 30);
foreach (PatternTools.HistogramHelper.HistogramBin b in hBins)
{
chartHistogram.Series[0].Points.AddXY(b.IntervalFloor, b.TheData.Count);
}
Console.WriteLine("Done first step");
List <double> pvalues = (from a in anovaResults
where a.MaxSignal > double.Parse(textBoxMinSignal.Text)
select a.PValue).ToList();
double correctedPValue = PatternTools.pTools.BenjaminiHochbergFDR((double)numericUpDownQValue.Value, pvalues, true);
labelpvaluecuttoff.Text = correctedPValue.ToString();
var toDisplay = from ar in anovaResults
select new
{
ID = ar.Locus,
MaxSignal = ar.MaxSignal,
DegreeOfFreedomBetweenGroups = ar.MyAnovaResult.DegreeOfFreedomBetweenGroups,
DegreesOfFredomTotal = ar.MyAnovaResult.DegreeOfFreedomTotal,
DegreeOfFreedomWithinGroups = ar.MyAnovaResult.DegreeOfFreedomWithinGroups,
MeanSquareVarianceBetweenGroups = ar.MyAnovaResult.MeanSquareVarianceBetweenGroups.ToString("E3"),
MeanSquareVarianceWithinGroups = ar.MyAnovaResult.MeanSquareVarianceWithinGroups.ToString("E3"),
SumOfSquaresBetweenGroups = ar.MyAnovaResult.SumOfSquaresBetweenGroups.ToString("E3"),
SumOfSquaresTotal = ar.MyAnovaResult.SumOfSquaresTotal.ToString("E3"),
SumOfSquaresWithingGroups = ar.MyAnovaResult.SumOfSquaresWithinGroups.ToString("E3"),
FCritical = ar.MyAnovaResult.FCriticalValue.ToString("E3"),
FRatio = ar.MyAnovaResult.FRatio.ToString("E3"),
PValue = ar.PValue,
StatisticallySignificant = ar.StatisticallySignificant(correctedPValue).ToString(),
Description = ar.Description
};
PatternTools.SortableBindingList <object> theList = new SortableBindingList <object>(toDisplay.ToList());
dataGridViewIDs.DataSource = theList;
PaintStatisticallySignificantRows();
Console.WriteLine("Total anova results successfully calculated: " + anovaResults.Count);
Console.WriteLine("Total proteins in index file: " + plp.MyIndex.TheIndexes.Count);
labelStatisticallySignificant.Text =
anovaResults.Count(a => a.StatisticallySignificant(correctedPValue) && a.MaxSignal > double.Parse(textBoxMinSignal.Text)) + " / " +
anovaResults.Count(a => a.StatisticallySignificant(correctedPValue)) + " / " +
anovaResults.Count;
//dataGridViewIDs.DataSource = loccus.ToList();
this.Update();
}
