public static float CorrelationTest(string file1, string file2, string arrayFile = "")
{
var list1 = DegradomeToRpkm(file1);
var list2 = DegradomeToRpkm(file2);
var intersectionKeys = list1.Keys.Intersect(list2.Keys).ToArray();
float[] farray1 = new float[intersectionKeys.Length];
float[] farray2 = new float[intersectionKeys.Length];
for (int i = 0; i < intersectionKeys.Length; i++)
{
farray1[i] = list1[intersectionKeys[i]];
farray2[i] = list2[intersectionKeys[i]];
}
if (!string.IsNullOrWhiteSpace(arrayFile))
{
float[,] matrix = new float[2, intersectionKeys.Length];
for (int i = 0; i < intersectionKeys.Length; i++)
{
matrix[0, i] = farray1[i];
matrix[1, i] = farray2[i];
}
CsvMatrix.Save(matrix, arrayFile);
}
return((float)Stats.CorrelationTest(farray1, farray2));
}
private void calculateButton_Click(object sender, EventArgs e)
{
//Compactness
double[,] x = CsvMatrix.Read(xTextBox.Text);
double[] compactnessArr = new double[files.Length];
resultTextBox.Text = string.Empty;
double[] mseArr = new double[files.Length];
mseResultTextBox.Text = string.Empty;
for (int i = 0; i < files.Length; i++)
{
int[] labels = FileExtension.Readlabels(files[i]);
compactnessArr[i] = Metrics.Compactness(x, labels);
mseArr[i] = Metrics.MeanSquaredError(x, labels);
resultTextBox.Text += compactnessArr[i].ToString() + "\r\n";
mseResultTextBox.Text += mseArr[i].ToString("0.00000000") + "\r\n";
}
if (files.Length > 1)
{
resultTextBox.Text += "Avg:" + compactnessArr.Average().ToString("0.00000000");
mseResultTextBox.Text += "Avg:" + mseArr.Average().ToString("0.00000000");
}
Clipboard.SetText(resultTextBox.Text + "\r\n" + mseResultTextBox.Text);
//Mean Squared Error
}
public void wt_3()
{
string[] files = new string[] {
@"U:\JICWork\kmedoids\length_71\wt\kmedoids_k_3_round_16_labels.csv",
@"U:\JICWork\kmedoids\length_71\wt\kmedoids_k_3_round_18_labels.csv",
@"U:\JICWork\kmedoids\length_71\wt\kmedoids_k_3_round_63_labels.csv",
@"U:\JICWork\kmedoids\length_71\wt\kmedoids_k_3_round_120_labels.csv",
@"U:\JICWork\kmedoids\length_71\wt\kmedoids_k_3_round_175_labels.csv"
};
string distanceMatrixFile = @"U:\JICWork\rna_distance_matrix_71_wt.txt";
double[,] distanceMatrix = CsvMatrix.Read(distanceMatrixFile);
Console.WriteLine("File, Compactness, Mean Squared Error");
foreach (string file in files)
{
int[] labels = FileExtension.Readlabels(file);
Console.Write(file);
Console.Write(",");
Console.Write(Metrics.CompactnessByDistanceMatrix(distanceMatrix, labels).ToString("0.000000"));
Console.Write(",");
Console.WriteLine(Metrics.MeanSquaredErrorByDistance(distanceMatrix, labels).ToString("0.000000"));
Console.Write("\r\n");
}
}
public static Sample[] GetMedoids(string labels_file, string dataset)
{
string x_file = $"{Config.WorkingFolder}\\cs_datasets\\{dataset}.csv";
double[,] x = CsvMatrix.Read(x_file);
int[] y = FileExtension.Readlabels(labels_file);
return(Metrics.GetMedoids(x, y));
}
private static double GetCompactnessByReactivity(string labels_file, DatasetCsv dataset)
{
string x_file = $"{Config.WorkingFolder}\\cs_datasets\\{dataset.XFile}";
double[,] x = CsvMatrix.Read(x_file);
int[] y = FileExtension.Readlabels(labels_file);
return(Metrics.Compactness(x, y));
}
private static double GetCompactnessByRnaDistance(string labels_file, DatasetCsv dataset)
{
string d_file = $"{Config.WorkingFolder}\\cs_datasets\\{dataset.XFile}";
double[,] d = CsvMatrix.Read(d_file);
int[] y = FileExtension.Readlabels(labels_file);
return(Metrics.CompactnessByDistanceMatrix(d, y));
}
public static void GenerateAverageReactivity()
{
foreach (DegradomeType dType in EnumUtil.GetValues <DegradomeType>())
{
double[,] matrix = CsvMatrix.Read($"{Config.WorkingFolder}cs_reactivity_{dType}_50.csv");
double[] average = new double[matrix.GetLength(1)];
double[] sdvArr = new double[matrix.GetLength(1)];
for (int col = 0; col < matrix.GetLength(1); col++)
{
//float sum = 0;
List <double> iCol = new List <double>();
for (int row = 0; row < matrix.GetLength(0); row++)
{
iCol.Add(matrix[row, col]);
//sum += matrix[row, col];
}
average[col] = iCol.Average();// sum / matrix.GetLength(0);
sdvArr[col] = iCol.StandardDeviation();
}
//save file
FileExtension.SaveList($"{Config.WorkingFolder}cs_reactivity_avg_{dType}_50.csv", average);
FileExtension.SaveList($"{Config.WorkingFolder}cs_reactivity_std_{dType}_50.csv", average);
}
}
