public void QTLPosition(int amountOfTraits, List <LineChartXY> charts, int amountOfChromosomes)
{
Dictionary <int, List <List <ObservablePoint> > > chromosomes = new Dictionary <int, List <List <ObservablePoint> > >();
for (int i = 0; i < amountOfChromosomes; i++)
{
//each list is a chromosome
List <List <ObservablePoint> > p = new List <List <ObservablePoint> >();
p.Add(new List <ObservablePoint>());
chromosomes.Add(i, p);
}
double maxVal = getLongestChr(this.db.GenomeOrganization.Chromosome, amountOfChromosomes);
foreach (LineChartXY chartXy in charts)
{
chartXy.AxisXTitle = "Position on chromosome";
chartXy.AxisYTitle = "-Log(P-Value)";
chartXy.SetXAxisMaxValue = maxVal;
}
double temp, tempLogVal = 0.0;
int chrNum = 0;
//we calcualte for the g traits the qtl position
for (int g = 0; g < amountOfTraits; g++)
{
//here we calculate to all of the markers its p value according to a a few traits
for (int i = 0; i < this.db.SubData[0].Genotype.Length; i++)
{
List <double> no = new List <double>();
List <double> n1 = new List <double>();
for (int k = 0; k < this.db.SubData.Count; k++)
{
if (this.db.SubData[k].Genotype[0, i] == 0)
{
no.Add(this.db.SubData[k].TraitValue[0, g]);
}
else if (this.db.SubData[k].Genotype[0, i] == 1)
{
n1.Add(this.db.SubData[k].TraitValue[0, g]);
}
//calculate the pvalue for trait and genotype and put in the correct bin
}
temp = StatisticCalculations.PValueTStatistic(no, n1);
tempLogVal = ((-1.0 * Math.Log(temp)));
chrNum = Convert.ToInt32(this.db.SubData[0].Locus[i].Position.Chromosome.Name);
if (chrNum <= amountOfChromosomes)
{
chrNum--;
int seriresNum = chromosomes[chrNum].Count - 1;
chromosomes[chrNum][seriresNum].Add(new ObservablePoint(this.db.SubData[0].Locus[i].Position.PositionChrGenetic, tempLogVal));
}
}
foreach (KeyValuePair <int, List <List <ObservablePoint> > > entry in chromosomes)
{
entry.Value.Add(new List <ObservablePoint>());
}
}
int counter = 0;
foreach (KeyValuePair <int, List <List <ObservablePoint> > > entry in chromosomes)
{
foreach (List <ObservablePoint> l in entry.Value)
{
l.Sort((x, y) => x.X.CompareTo(y.X));
charts[counter].AddLineChart(l, 5);
}
counter++;
}
}
public void PValueHistogram(CartesianChart chart)
{
if (PValhistChart == null)
{
PValhistChart = new HistogramChart(chart);
}
PValhistChart.AxisXTitle = "P-Value";
PValhistChart.AxisYTitle = "Proportion of Markers %";
PValhistChart.RemvoeColumnSeries();
int twentyPercent = 0;
int fortyPercent = 0;
int sixtyPercent = 0;
int eightyPercent = 0;
int oneHundrerdPercent = 0;
double temp = 0.0;
double popSize = (db.SubData[0].Genotype.Length) * (db.SubData[0].TraitValue.Length) * 1.0;
//go over all the individuals of first marker and first trait and calculate p value
//get the answer and put it in the correct bin
for (int i = 0; i < this.db.SubData[0].Genotype.Length; i++)
{
//we get the wanted genotype index
for (int j = 0; j < this.db.SubData[0].TraitValue.Length; j++)
{
//we get the wanted trait index
List <double> no = new List <double>();
List <double> n1 = new List <double>();
for (int k = 0; k < this.db.SubData.Count; k++)
{
if (this.db.SubData[k].Genotype[0, i] == 0)
{
no.Add(this.db.SubData[k].TraitValue[0, j]);
}
else if (this.db.SubData[k].Genotype[0, i] == 1)
{
n1.Add(this.db.SubData[k].TraitValue[0, j]);
}
//iterate over all the people and gather two groups of n0 and n1
}
//calculate the pvalue for trait and genotype and put in the correct bin
//temp=result of p value
temp = StatisticCalculations.PValueTStatistic(no, n1);
pLogValues.Add((-1.0 * Math.Log(temp)));
if (temp >= 0.0 && temp < 0.2)
{
twentyPercent++;
}
else if (temp >= 0.2 && temp < 0.4)
{
fortyPercent++;
}
else if (temp >= 0.4 && temp < 0.6)
{
sixtyPercent++;
}
else if (temp >= 0.6 && temp < 0.8)
{
eightyPercent++;
}
else if (temp >= 0.8 && temp <= 1.0)
{
oneHundrerdPercent++;
}
}
}
List <double> pValues = new List <double>();
pValues.Add(twentyPercent / popSize);
pValues.Add(fortyPercent / popSize);
pValues.Add(sixtyPercent / popSize);
pValues.Add(eightyPercent / popSize);
pValues.Add(oneHundrerdPercent / popSize);
List <string> pTitles = new List <string>();
pTitles.Add("0-20%");
pTitles.Add("20-40%");
pTitles.Add("40-60%");
pTitles.Add("60-80%");
pTitles.Add("80-100%");
PValhistChart.AddColumnSeries(pTitles, pValues, ColorConstants.highliteColor);
}
