public void ChiSquaredHistogramChart(CartesianChart chart)
{
if (histChartChi == null)
{
histChartChi = new HistogramChart(chart);
}
histChartChi.AxisXTitle = "Chi^2 statistic";
histChartChi.AxisYTitle = "Proportion of markers";
double chiVal = 0;
double chiExpected = 0;
double counterN0 = 0, counterN1 = 0;
int twentyPercent = 0;
int fortyPercent = 0;
int sixtyPercent = 0;
int eightyPercent = 0;
int oneHundrerdPercent = 0;
double popSize = this.db.SubData[0].Genotype.Length * 1.0;
// this is our 100%
//we iterate over all the population
for (int i = 0; i < this.db.SubData[0].Genotype.Length; i++)
{
counterN0 = 0;
counterN1 = 0;
chiVal = 0;
chiExpected = 0;
//we iterate over the genotype of each person
for (int j = 0; j < this.db.SubData.Count; j++)
{
if (this.db.SubData[j].Genotype[0, i] == 0)
{
counterN0++;
}
else if (this.db.SubData[j].Genotype[0, i] == 1)
{
counterN1++;
}
}
//we finished going over the persons genotype divide by the 100 percent and add to the relevant bucket
chiExpected = (counterN0 + counterN1) / 2;
chiVal = (Math.Pow((counterN0 - chiExpected), 2.0) + Math.Pow((counterN1 - chiExpected), 2.0)) / chiExpected;
if (chiVal >= 0.0 && chiVal < 0.2)
{
twentyPercent++;
}
else if (chiVal >= 0.2 && chiVal < 0.4)
{
fortyPercent++;
}
else if (chiVal >= 0.4 && chiVal < 0.6)
{
sixtyPercent++;
}
else if (chiVal >= 0.6 && chiVal < 0.8)
{
eightyPercent++;
}
else if (chiVal >= 0.8 && chiVal <= 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%");
histChartChi.AddColumnSeries(pTitles, pValues, ColorConstants.highliteColor);
}
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 SegregationMarkerHistogram(CartesianChart chart)
{
HistogramChart histChart = new HistogramChart(chart);
histChart.AxisXTitle = " n0/(n1+n0)";
histChart.AxisYTitle = "Proportion of Markers %";
int twentyPercent = 0, fortyPercent = 0, sixtyPercent = 0, eightyPercent = 0, oneHundrerdPercent = 0;
double temp, counterN0 = 0, counterN1 = 0;
double genotypeSize = db.SubData[0].Genotype.Length;
//we iterate over all the population
for (int i = 0; i < this.db.SubData[0].Genotype.Length; i++)
{
counterN0 = 0;
counterN1 = 0;
//we iterate over the genotype of each person
for (int j = 0; j < this.db.SubData.Count; j++)
{
if (this.db.SubData[j].Genotype[0, i] == 0)
{
counterN0++;
}
else if (this.db.SubData[j].Genotype[0, i] == 1)
{
counterN1++;
}
}
//we finished going over the persons genotype divide by the 100 percent and add to the relevant bucket
temp = counterN0 / (counterN1 + counterN0);
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 <string> titles = new List <string>();
titles.Add("0-20%");
titles.Add("20-40%");
titles.Add("40-60%");
titles.Add("60-80%");
titles.Add("80-100%");
List <double> values = new List <double>();
values.Add(twentyPercent / genotypeSize);
values.Add(fortyPercent / genotypeSize);
values.Add(sixtyPercent / genotypeSize);
values.Add(eightyPercent / genotypeSize);
values.Add(oneHundrerdPercent / genotypeSize);
histChart.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);
}
public void MarkerQualityHistogram(CartesianChart chart)
{
HistogramChart histChart = new HistogramChart(chart);
histChart.AxisXTitle = " Missing Data %";
histChart.AxisYTitle = "Proportion of Markers %";
// find out which markers are:
//0-20%
//20-40%
//40-60%
//60-80%
//80-100%
int twentyPercent = 0;
int fortyPercent = 0;
int sixtyPercent = 0;
int eightyPercent = 0;
int oneHundrerdPercent = 0;
double popSize = db.SubData.Count * 1.0;
double temp;
double counter = 0;
// this is our 100%
double genotypeSize = db.SubData[0].Genotype.Length;
//we iterate over all the population
for (int i = 0; i < this.db.SubData.Count; i++)
{
counter = 0;
//we iterate over the genotype of each person
for (int j = 0; j < this.db.SubData[i].Genotype.Length; j++)
{
if (this.db.SubData[i].GenotypeOk[0, j] == true)
{
counter++;
}
}
//we finished going over the persons genotype divide by the 100 percent and add to the relevant bucket
temp = counter / genotypeSize;
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++;
}
}
//we have all the data now we arrange it in the format the histogram has to accept
List <string> titles = new List <string>();
titles.Add("0-20%");
titles.Add("20-40%");
titles.Add("40-60%");
titles.Add("60-80%");
titles.Add("80-100%");
List <double> values = new List <double>();
values.Add(twentyPercent / popSize);
values.Add(fortyPercent / popSize);
values.Add(sixtyPercent / popSize);
values.Add(eightyPercent / popSize);
values.Add(oneHundrerdPercent / popSize);
histChart.AddColumnSeries(titles, values, ColorConstants.highliteColor);
}