public static void Run(bool removeNA, bool replaceNA, string missingValPercent, string missingValReplace,
ProgressWindow progressWindow, Dictionary <string, Dictionary <string, string> > dataMap,
IsotopeCalc isotopeCalc)
{
var excelPkg = new ExcelPackage();
FormatToColumns(excelPkg, dataMap);
if (removeNA)
{
progressWindow.progressTextBox.AppendLine("Removing NA");
RemoveNA(excelPkg, missingValPercent, dataMap);
}
if (replaceNA)
{
progressWindow.progressTextBox.AppendLine($"Replacing NA with {missingValReplace}...");
ReplaceNA(excelPkg, "Compounds Detected", missingValReplace);
}
if (isotopeCalc.isotopeToCompound.Count > 0)
{
progressWindow.progressTextBox.AppendLine("Calculating ratios");
CalculateRatios(excelPkg, isotopeCalc, dataMap);
}
progressWindow.progressTextBox.AppendLine("Calculating concentrations");
Concentration(excelPkg, isotopeCalc);
// More WriteOutputFile....
progressWindow.progressTextBox.AppendLine("Done");
progressWindow.UseWaitCursor = false;
}
/// <summary>
/// Calculates the ratio compound area / isotope area.
/// </summary>
/// <param name="excelPkg"></param>
/// <param name="isotopeCalc"></param>
/// <param name="detectedMap"></param>
public static void CalculateRatios(ExcelPackage excelPkg, IsotopeCalc isotopeCalc,
Dictionary <string, Dictionary <string, string> > detectedMap)
{
var compoundList = new List <string>(detectedMap.Keys);
var sampleList = new List <string>(detectedMap[compoundList[0]].Keys);
int numSamples = sampleList.Count;
// Write data to new excel worksheet
var isotopeRatioSheet = excelPkg.Workbook.Worksheets.Add("Isotope Ratio");
isotopeRatioSheet.Cells[1, 1].Value = "Sample";
// Fill in sample names
for (int r = 2; r <= numSamples + 1; r++)
{
isotopeRatioSheet.Cells[r, 1].Value = sampleList[r - 2]; // Write sample name in first column
}
int col = 2;
foreach (var isotope in isotopeCalc.isotopeToCompound.Keys)
{
foreach (var compound in isotopeCalc.isotopeToCompound[isotope].Where(compound => compoundList.Contains(compound)))
{
isotopeRatioSheet.Cells[1, col].Value = compound; // Put compound name in first row
for (int row = 2; row <= numSamples + 1; row++) // Fill in sample ratios
{
// Get area value from map with compound/sample match
var sampleName = isotopeRatioSheet.Cells[row, 1].Value.ToString();
detectedMap[compound].TryGetValue(sampleName, out var compoundArea);
if (double.TryParse(compoundArea, out var compoundAreaNum))
{
detectedMap[isotope].TryGetValue(sampleName, out var isotopeArea);
if (double.TryParse(isotopeArea, out var isotopeAreaNum))
{
isotopeRatioSheet.Cells[row, col].Value = compoundAreaNum / isotopeAreaNum;
}
else
{
isotopeRatioSheet.Cells[row, col].Value = "No Isotope";
}
}
else
{
isotopeRatioSheet.Cells[row, col].Value = 0.0;
}
}
col++;
}
}
isotopeRatioSheet.Cells[2, 2, numSamples + 1, col - 1].Style.Numberformat.Format = "0.000000";
isotopeRatioSheet.Cells.AutoFitColumns();
SaveFile(excelPkg, outputFileName);
}
public static void Concentration(ExcelPackage excelPkg, IsotopeCalc isotopeCalc)
{
// Copy ratios data to new sheet to do calculation
var concentrationSheet = excelPkg.Workbook.Worksheets.Copy("Isotope Ratio", "Concentrations");
var rows = concentrationSheet.Dimension.Rows;
var cols = concentrationSheet.Dimension.Columns;
// Iterate through compounds
int col = 2;
for (int c = 2; c <= cols; c++)
{
var compound = concentrationSheet.Cells[1, c].Text;
// Get slope and intercept for compound
var slopeIntercept = isotopeCalc.SlopeIntercept("filePath", compound);
// Calculate for each sample
for (int r = 2; r <= rows; r++)
{
var ratio = concentrationSheet.Cells[r, c].Text;
if (double.TryParse(ratio, out var ratioNum))
{
if (ratioNum == 0.0)
{
concentrationSheet.Cells[r, c].Value = 0.0;
}
else
{
concentrationSheet.Cells[r, c].Value = (ratioNum - slopeIntercept[1]) / slopeIntercept[0];
}
}
}
}
//isotopeRatioSheet.Cells[2, 2, numSamples + 1, numCompounds + 1].Style.Numberformat.Format = "0.000000";
concentrationSheet.Cells.AutoFitColumns();
SaveFile(excelPkg, outputFileName);
}
private void submitButton_Click(object sender, EventArgs e)
{
if (filePath == string.Empty)
{
return;
}
var progressWindow = new ProgressWindow();
progressWindow.Show();
// Create isotope map
Dictionary <string, List <string> > isotopeMap = null;
IsotopeCalc isotopeCalc = new IsotopeCalc();
//isotopeMap = isotopeCalc.IsotopeMap(filePath);
// Read data to map
Dictionary <string, Dictionary <string, string> > dataMap = null;
if (skylineRadioButton.Checked)
{
dataMap = ProcessSkyline.ReadDataToMap(filePath);
if (dataMap.Count == 0)
{
return;
}
// Create isotope map
isotopeMap = isotopeCalc.IsotopeMap(filePath);
}
else if (sciexRadioButton.Checked)
{
dataMap = ProcessSciex.ReadDataToMap(filePath);
if (dataMap.Count == 0)
{
return;
}
}
else if (NormQcRadioButton.Checked)
{
dataMap = ProcessSciex.ReadDataToMap(filePath);
//Normalize.NormalizeToQC(filePath, dataMap);
}
else if (multiquantTxtRadioButton.Checked)
{
dataMap = ReadInput.ReadMultiQuantTxt(filePaths);
var templatePath = Environment.GetFolderPath(Environment.SpecialFolder.Desktop) +
$"\\DataProcessor\\targeted_300_template-serum-mrm.xlsx";
WriteOutputFile.WriteMapToSheetCompoundsInRows(progressWindow, dataMap, templatePath, "Relative Quant Data", 1);
//WriteOutputFile.WriteMapToSheetCompoundsInRows(progressWindow, dataMap, templatePath, "Data Reproducibility", 2);
}
if (dataMap == null)
{
progressWindow.progressTextBox.AppendLine("Error reading file.");
return;
}
progressWindow.progressTextBox.AppendLine("Finished reading data.\r\nWriting data");
bool removeNA = removeMissingCheckBox.Checked;
var missingValPercent = string.IsNullOrEmpty(missingValueBox.Text)
? missingValueBox.PlaceholderText
: missingValueBox.Text;
bool replaceNA = replaceMissingValueCheckBox.Checked;
var missingValReplace = string.IsNullOrEmpty(replaceMissingValueTextBox.Text)
? replaceMissingValueTextBox.PlaceholderText
: replaceMissingValueTextBox.Text;
//WriteOutputFile.WriteSciex(replaceNA, missingValReplace, progressWindow, dataMap, Environment.GetFolderPath(Environment.SpecialFolder.Desktop) + $"\\DataProcessor\\targeted_300_template-tissue.xlsx");
WriteOutputFile.Run(removeNA, replaceNA, missingValPercent, missingValReplace, progressWindow, dataMap, isotopeCalc);
}