private void extractPhenotypesOfInterestToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
FormClassification WindowClassification = new FormClassification(CompleteScreening);
WindowClassification.label1.Text = "Class";
WindowClassification.Text = "Phenotypes of Interest";
WindowClassification.buttonClassification.Text = "Display";
if (WindowClassification.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int SelectedClass = WindowClassification.comboBoxForNeutralClass.SelectedIndex;
List<string> ListDescName = new List<string>();
ListDescName.Add("Idx");
ListDescName.Add("Plate");
ListDescName.Add("Pos X");
ListDescName.Add("Pos Y");
ListDescName.AddRange(CompleteScreening.ListDescriptors.GetListNameActives());
List<string[]> ListValues = new List<string[]>();
int Idx = 0;
foreach (cPlate TmpPlate in CompleteScreening.ListPlatesActive)
{
foreach (cWell TmpWell in TmpPlate.ListActiveWells)
{
if (TmpWell.GetClass() == SelectedClass)
{
List<string> LValues = new List<string>();
LValues.Add(Idx.ToString());
LValues.Add(TmpPlate.Name);
LValues.Add(TmpWell.GetPosX().ToString());
LValues.Add(TmpWell.GetPosY().ToString());
for (int IdxDesc = 0; IdxDesc < CompleteScreening.ListDescriptors.Count; IdxDesc++)
{
if (CompleteScreening.ListDescriptors[IdxDesc].IsActive())
{
double Value = TmpWell.GetAverageValuesList(false)[IdxDesc];
LValues.Add(Value.ToString());
}
}
ListValues.Add(LValues.ToArray());
Idx++;
}
}
}
cDisplayTable WindowDisplayTable = new cDisplayTable("Phenotypes of Interest. Class " + SelectedClass, ListDescName.ToArray(), ListValues, GlobalInfo, false);
WindowDisplayTable.Show();
}
private void ComputeAndDisplayPCA(cExtendPlateList PlatesToProcess)
{
if (CompleteScreening == null) return;
FormClassification WindowClassification = new FormClassification(CompleteScreening);
WindowClassification.label1.Text = "Class of interest";
WindowClassification.Text = "PCA";
WindowClassification.buttonClassification.Text = "Process";
if (WindowClassification.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int NeutralClass = WindowClassification.comboBoxForNeutralClass.SelectedIndex;
int NumWell = 0;
int NumWellForLearning = 0;
foreach (cPlate CurrentPlate in PlatesToProcess)
{
foreach (cWell CurrentWell in CurrentPlate.ListActiveWells)
{
if (CurrentWell.GetClass() == NeutralClass)
NumWellForLearning++;
}
NumWell += CurrentPlate.GetNumberOfActiveWells();
}
if (NumWellForLearning == 0)
{
MessageBox.Show("No well of the selected class identified", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
int NumDesc = CompleteScreening.GetNumberOfActiveDescriptor();
if (NumDesc <= 1)
{
MessageBox.Show("More than one descriptor are required for this operation", "Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
return;
}
double[,] DataForPCA = new double[NumWellForLearning, CompleteScreening.GetNumberOfActiveDescriptor() + 1];
// return;
Matrix EigenVectors = PCAComputation(DataForPCA, NumWellForLearning, NumWell, NumDesc, NeutralClass, PlatesToProcess);
if (EigenVectors == null) return;
SimpleForm NewWindow = new SimpleForm(CompleteScreening);
Series CurrentSeries = new Series();
CurrentSeries.ShadowOffset = 1;
Matrix CurrentPt = new Matrix(NumWell, NumDesc);
DataForPCA = new double[NumWell, NumDesc + 1];
for (int desc = 0; desc < NumDesc; desc++)
{
if (CompleteScreening.ListDescriptors[desc].IsActive() == false) continue;
List<double> CurrentDesc = new List<double>();
foreach (cPlate CurrentPlate in PlatesToProcess)
{
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = CurrentPlate.GetWell(IdxValue, IdxValue0, true);
if (TmpWell == null) continue;
CurrentDesc.Add(TmpWell.ListDescriptors[desc].GetValue());
}
}
for (int i = 0; i < NumWell; i++)
DataForPCA[i, desc] = CurrentDesc[i];
}
int IDx = 0;
foreach (cPlate CurrentPlate in PlatesToProcess)
{
for (int IdxValue = 0; IdxValue < CompleteScreening.Columns; IdxValue++)
for (int IdxValue0 = 0; IdxValue0 < CompleteScreening.Rows; IdxValue0++)
{
cWell TmpWell = CurrentPlate.GetWell(IdxValue, IdxValue0, true);
if (TmpWell == null) continue;
DataForPCA[IDx++, NumDesc] = TmpWell.GetClass();
}
}
for (int i = 0; i < NumWell; i++)
for (int j = 0; j < NumDesc; j++) CurrentPt.addElement(i, j, DataForPCA[i, j]);
Matrix NewPt = new Matrix(NumWell, NumDesc);
NewPt = CurrentPt.multiply(EigenVectors);
double MinY = double.MaxValue, MaxY = double.MinValue;
for (int IdxValue0 = 0; IdxValue0 < NumWell; IdxValue0++)
{
double CurrentY = NewPt.getElement(IdxValue0, 1);
if (CurrentY < MinY) MinY = CurrentY;
if (CurrentY > MaxY) MaxY = CurrentY;
CurrentSeries.Points.AddXY(NewPt.getElement(IdxValue0, 0), CurrentY);
CurrentSeries.Points[IdxValue0].Color = CompleteScreening.GlobalInfo.GetColor((int)DataForPCA[IdxValue0, NumDesc]);
CurrentSeries.Points[IdxValue0].MarkerStyle = MarkerStyle.Circle;
CurrentSeries.Points[IdxValue0].MarkerSize = 8;
}
ChartArea CurrentChartArea = new ChartArea();
CurrentChartArea.BorderColor = Color.Black;
NewWindow.chartForSimpleForm.ChartAreas.Add(CurrentChartArea);
NewWindow.chartForSimpleForm.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
CurrentChartArea.BackColor = Color.FromArgb(164, 164, 164);
string AxeName = "";
int IDxDesc = 0;
for (int Desc = 0; Desc < CompleteScreening.ListDescriptors.Count; Desc++)
{
if (CompleteScreening.ListDescriptors[Desc].IsActive() == false) continue;
AxeName += String.Format("{0:0.###}", EigenVectors.getElement(IDxDesc++, 0)) + "x" + CompleteScreening.ListDescriptors[Desc].GetName() + " + ";
// AxeName += String.Format("{0:0.##}", EigenVectors.getElement(CompleteScreening.ListDescriptors.Count - 1, 0)) + "x" + CompleteScreening.ListDescriptorName[CompleteScreening.ListDescriptors.Count - 1];
}
CurrentChartArea.Axes[0].Title = AxeName.Remove(AxeName.Length - 3);
CurrentChartArea.Axes[0].MajorGrid.Enabled = true;
AxeName = "";
IDxDesc = 0;
for (int Desc = 0; Desc < CompleteScreening.ListDescriptors.Count; Desc++)
{
if (CompleteScreening.ListDescriptors[Desc].IsActive() == false) continue;
AxeName += String.Format("{0:0.###}", EigenVectors.getElement(IDxDesc++, 1)) + "x" + CompleteScreening.ListDescriptors[Desc].GetName() + " + ";
}
//AxeName += String.Format("{0:0.##}", EigenVectors.getElement(CompleteScreening.ListDescriptors.Count - 1, 0)) + "x" + CompleteScreening.ListDescriptorName[CompleteScreening.ListDescriptors.Count - 1];
CurrentChartArea.Axes[1].Title = AxeName.Remove(AxeName.Length - 3);
CurrentChartArea.Axes[1].MajorGrid.Enabled = true;
CurrentChartArea.Axes[1].Minimum = MinY;
CurrentChartArea.Axes[1].Maximum = MaxY;
CurrentChartArea.AxisX.LabelStyle.Format = "N2";
CurrentChartArea.AxisY.LabelStyle.Format = "N2";
CurrentSeries.ChartType = SeriesChartType.Point;
if (GlobalInfo.OptionsWindow.checkBoxDisplayFastPerformance.Checked) CurrentSeries.ChartType = SeriesChartType.FastPoint;
NewWindow.chartForSimpleForm.Series.Add(CurrentSeries);
NewWindow.Text = "PCA";
NewWindow.Show();
NewWindow.chartForSimpleForm.Update();
NewWindow.chartForSimpleForm.Show();
NewWindow.Controls.AddRange(new System.Windows.Forms.Control[] { NewWindow.chartForSimpleForm });
}
/// <summary>
/// This function displays the evolution of the average value of a certain descriptor through the plates, for a specified class
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void descriptorEvolutionToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
FormClassification WindowClassification = new FormClassification(CompleteScreening);
WindowClassification.label1.Text = "Class";
WindowClassification.Text = CompleteScreening.ListDescriptors[CompleteScreening.ListDescriptors.CurrentSelectedDescriptor].GetName() + " evolution";
WindowClassification.buttonClassification.Text = "Display";
if (WindowClassification.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
int SelectedClass = WindowClassification.comboBoxForNeutralClass.SelectedIndex;
cExtendedList ListValuePerWell = new cExtendedList();
List<cDescriptor> List_Averages = new List<cDescriptor>();
cWell TempWell;
int Desc = this.comboBoxDescriptorToDisplay.SelectedIndex;
int NumberOfPlates = CompleteScreening.ListPlatesActive.Count;
Series CurrentSeries = new Series();
CurrentSeries.Name = "Series1";
CurrentSeries.ChartType = SeriesChartType.ErrorBar;
CurrentSeries.ShadowOffset = 1;
Series SeriesLine = new Series();
SeriesLine.Name = "SeriesLine";
SeriesLine.ShadowOffset = 1;
SeriesLine.ChartType = SeriesChartType.Line;
int RealPlateIdx = 0;
// loop on all the plates
for (int PlateIdx = 0; PlateIdx < NumberOfPlates; PlateIdx++)
{
cPlate CurrentPlateToProcess = CompleteScreening.ListPlatesActive.GetPlate(CompleteScreening.ListPlatesActive[PlateIdx].Name);
ListValuePerWell.Clear();
for (int row = 0; row < CompleteScreening.Rows; row++)
for (int col = 0; col < CompleteScreening.Columns; col++)
{
TempWell = CurrentPlateToProcess.GetWell(col, row, true);
if (TempWell == null) continue;
else
{
if (TempWell.GetClass() == SelectedClass)
{
double Val = TempWell.ListDescriptors[Desc].GetValue();
if (double.IsNaN(Val)) continue;
ListValuePerWell.Add(Val);
}
}
}
if (ListValuePerWell.Count >= 1)
{
DataPoint CurrentPt = new DataPoint();
CurrentPt.XValue = RealPlateIdx;
double[] Values = new double[3];
Values[0] = ListValuePerWell.Mean();
double Std = ListValuePerWell.Std();
if (double.IsInfinity(Std) || (double.IsNaN(Std))) Std = 0;
Values[1] = Values[0] - Std;
Values[2] = Values[0] + Std;
CurrentPt.YValues = Values;//ListValuePerWell.ToArray();
CurrentSeries.Points.Add(CurrentPt);
CurrentSeries.Points[RealPlateIdx].AxisLabel = CurrentPlateToProcess.Name;
CurrentSeries.Points[RealPlateIdx].Font = new Font("Arial", 8);
CurrentSeries.Points[RealPlateIdx].Color = CompleteScreening.GlobalInfo.GetColor(SelectedClass);
SeriesLine.Points.AddXY(RealPlateIdx, Values[0]);
SeriesLine.Points[RealPlateIdx].ToolTip = "Plate name: " + CurrentPlateToProcess.Name + "\nAverage: " + string.Format("{0:0.###}", Values[0]) + "\nStdev: " + string.Format("{0:0.###}", Std);
SeriesLine.Points[RealPlateIdx].Font = new Font("Arial", 8);
SeriesLine.Points[RealPlateIdx].BorderColor = Color.Black;
SeriesLine.Points[RealPlateIdx].MarkerStyle = MarkerStyle.Circle;
SeriesLine.Points[RealPlateIdx].MarkerSize = 8;
RealPlateIdx++;
}
}
SimpleForm NewWindow = new SimpleForm(CompleteScreening);
int thisWidth = 200 * SeriesLine.Points.Count;
if (thisWidth > 1500) thisWidth = 1500;
NewWindow.Width = thisWidth;
NewWindow.Height = 400;
ChartArea CurrentChartArea = new ChartArea();
CurrentChartArea.BorderColor = Color.Black;
NewWindow.chartForSimpleForm.ChartAreas.Add(CurrentChartArea);
CurrentChartArea.AxisX.Interval = 1;
CurrentChartArea.Axes[1].IsMarksNextToAxis = true;
CurrentChartArea.Axes[1].Title = CompleteScreening.ListDescriptors[CompleteScreening.ListDescriptors.CurrentSelectedDescriptor].GetName();
CurrentChartArea.Axes[0].MajorGrid.Enabled = false;
CurrentChartArea.Axes[1].MajorGrid.Enabled = false;
NewWindow.chartForSimpleForm.TextAntiAliasingQuality = TextAntiAliasingQuality.High;
CurrentChartArea.BackGradientStyle = GradientStyle.TopBottom;
CurrentChartArea.BackColor = CompleteScreening.GlobalInfo.OptionsWindow.panel1.BackColor;
CurrentChartArea.BackSecondaryColor = Color.White;
CurrentSeries["BoxPlotWhiskerPercentile"] = "false";
CurrentSeries["BoxPlotShowMedian"] = "false";
CurrentSeries["BoxPlotWhiskerPercentile"] = "false";
CurrentSeries["BoxPlotShowAverage"] = "false";
CurrentSeries["BoxPlotPercentile"] = "false";
CurrentChartArea.AxisX.IsLabelAutoFit = true;
NewWindow.chartForSimpleForm.Series.Add(CurrentSeries);
NewWindow.chartForSimpleForm.Series.Add(SeriesLine);
Title CurrentTitle = new Title("Class " + SelectedClass + " " + CurrentChartArea.Axes[1].Title + " evolution");
NewWindow.chartForSimpleForm.Titles.Add(CurrentTitle);
NewWindow.chartForSimpleForm.Titles[0].Font = new Font("Arial", 9);
NewWindow.Show();
NewWindow.chartForSimpleForm.Update();
NewWindow.chartForSimpleForm.Show();
NewWindow.Controls.AddRange(new System.Windows.Forms.Control[] { NewWindow.chartForSimpleForm });
return;
}
private void coeffOfVariationEvolutionToolStripMenuItem_Click(object sender, EventArgs e)
{
if (CompleteScreening == null) return;
FormClassification WinForClass = new FormClassification(CompleteScreening);
WinForClass.buttonClassification.Text = "Display";
WinForClass.Text = "Select the class of interest";
WinForClass.label1.Text = "Class";
if (WinForClass.ShowDialog() != System.Windows.Forms.DialogResult.OK) return;
BuildCV(this.comboBoxDescriptorToDisplay.SelectedIndex, WinForClass.comboBoxForNeutralClass.SelectedIndex).Show();
}
