public void TraitDistributionHistogram(int traitIndex, CartesianChart chart)
{
if (traitHistogramDist == null)
{
traitHistogramDist = new HistogramChart(chart);
}
traitHistogramDist.AxisXTitle = "Trait Values";
traitHistogramDist.AxisYTitle = "Proportion of Individuals";
traitHistogramDist.RemvoeColumnSeries();
double max, min;
max = db.SubData[0].TraitValue[0, traitIndex];
min = db.SubData[0].TraitValue[0, traitIndex];
double popSize = 0.0;
// make sure that our population is according to the size of the traits that we actually have info about them
foreach (DataIndividualsAndTraits ind in db.SubData)
{
if (ind.TraitValueOk[0, traitIndex] == true)
{
popSize++;
}
}
for (int i = 0; i < db.SubData.Count; i++)
{
if (db.SubData[i].TraitValue[0, traitIndex] > max && db.SubData[i].TraitValueOk[0, traitIndex] == true)
{
max = db.SubData[i].TraitValue[0, traitIndex];
}
}
double twentyPrecent = 0.0, fortyPrecent = 0.0, sixtyPrecent = 0.0, eightPrecent = 0.0, onehundredPrecent = 0.0;
for (int i = 0; i < this.db.SubData.Count; i++)
{
double temp = db.SubData[i].TraitValue[0, traitIndex];
temp = temp / max;
if (temp >= 0.0 && temp < 0.2 && db.SubData[i].TraitValueOk[0, traitIndex] == true)
{
twentyPrecent++;
}
else if (temp >= 0.2 && temp < 0.4 && db.SubData[i].TraitValueOk[0, traitIndex] == true)
{
fortyPrecent++;
}
else if (temp >= 0.4 && temp < 0.6 && db.SubData[i].TraitValueOk[0, traitIndex] == true)
{
sixtyPrecent++;
}
else if (temp >= 0.6 && temp < 0.8 && db.SubData[i].TraitValueOk[0, traitIndex] == true)
{
eightPrecent++;
}
else if (temp >= 0.8 && temp < 1.0 && db.SubData[i].TraitValueOk[0, traitIndex] == true)
{
onehundredPrecent++;
}
}
//get the proportion of the indivivuals
List <string> titles = new List <string>();
titles.Add("0.0-" + (max * 0.2).ToString("0.00"));
titles.Add((max * 0.2).ToString("0.00") + "-" + (max * 0.4).ToString("0.00"));
titles.Add((max * 0.4).ToString("0.00") + "-" + (max * 0.6).ToString("0.00"));
titles.Add((max * 0.6).ToString("0.00") + "-" + (max * 0.8).ToString("0.00"));
titles.Add((max * 0.8).ToString("0.00") + "-" + (max).ToString("0.00"));
List <double> values = new List <double>();
values.Add(twentyPrecent / popSize);
values.Add(fortyPrecent / popSize);
values.Add(sixtyPrecent / popSize);
values.Add(eightPrecent / popSize);
values.Add(onehundredPrecent / popSize);
traitHistogramDist.AddColumnSeries(titles, values, ColorConstants.highliteColor);
}
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);
}