//gene enrichment analysis for both Basic PECA and PECA-N
public static IMatrixData GetGOEnr(IMatrixData mdata, string workingDir, int option)//, out string errString)
{
char separator = '\t';
string filename = Path.Combine(workingDir, @".\Goterms.txt");
IMatrixData mNew = (IMatrixData)mdata.CreateNewInstance();
string name = "GSA";
if (option == 0)
{
name = name + "_Degradation";
}
else if (option == 1)
{
name = name + "_Synthesis";
}
mNew.Clear();
mNew.Name = name;
mNew.AltName = name;
//update
//mNew.AltName = "Gene Set Enrichment Analysis";
//mNew.Description = "Gene Set Enrichment Analysis";
string[] colNames = TabSep.GetColumnNames(filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, null, separator);
string[][] cols = TabSep.GetColumns(colNames, filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, separator);
int nrows = TabSep.GetRowCount(filename);
mNew.Values.Init(nrows, 0);
mNew.SetAnnotationColumns(new List <string>(colNames), new List <string>(colNames), new List <string[]>(cols), new List <string>(),
new List <string>(), new List <string[][]>(), new List <string>(), new List <string>(), new List <double[]>(),
new List <string>(), new List <string>(), new List <double[][]>());
//convert the ones not matching regex to numeric
string pattern = @"^((?!id|name|members).)*$";
Regex numericReg = new Regex(pattern);
List <int> numericList = new List <int>();
for (int i = 0; i < colNames.Length; i++)
{
if (numericReg.Match(colNames[i]).Success)
{
numericList.Add(i);
}
}
StringToNumerical(numericList, mNew);
return(mNew);
}
private static void CreateMatrixData(CountingResult result, IMatrixData data, int minCount, IEnumerable selection)
{
List <string[]> type = new List <string[]>();
List <string[]> name = new List <string[]>();
List <double> count = new List <double>();
List <double> percOfTotal = new List <double>();
List <double> selCount = new List <double>();
List <double> selPerc = new List <double>();
for (int i = 0; i < result.Count; i++)
{
int c = result.GetTotalCountAt(i);
if (c < minCount)
{
continue;
}
type.Add(new[] { result.GetType1At(i) });
name.Add(new[] { result.GetName1At(i) });
count.Add(c);
percOfTotal.Add(Math.Round(10000.0 * c / data.RowCount) / 100.0);
if (selection != null)
{
int c1 = result.GetSelectCountAt(i);
selCount.Add(c1);
selPerc.Add(Math.Round(1000.0 * c1 / c) / 10.0);
}
}
double[,] ex = new double[type.Count, 0];
List <string[][]> catCols = new List <string[][]> {
type.ToArray(), name.ToArray()
};
List <string> catColNames = new List <string>(new[] { "Type", "Name" });
List <double[]> numCols = new List <double[]> {
count.ToArray(), percOfTotal.ToArray()
};
if (selection != null)
{
numCols.Add(selCount.ToArray());
numCols.Add(selPerc.ToArray());
}
List <string> numColNames = new List <string>(new[] { "Count", "Percentage of total" });
if (selection != null)
{
numColNames.AddRange(new[] { "Selection count", "Selection percentage" });
}
data.Clear();
data.Name = "Count";
data.ColumnNames = new List <string>();
data.Values.Set(ex);
data.SetAnnotationColumns(new List <string>(), new List <string[]>(), catColNames, catCols, numColNames, numCols,
new List <string>(), new List <double[][]>());
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
int[] cols = param.GetParam <int[]>("Columns").Value;
HashSet <int> w = ArrayUtils.ToHashSet(param.GetParam <int[]>("Calculate").Value);
bool[] include = new bool[SummaryStatisticsRows.procs.Length];
double[][] rowws = new double[SummaryStatisticsRows.procs.Length][];
for (int i = 0; i < include.Length; i++)
{
include[i] = w.Contains(i);
if (include[i])
{
rowws[i] = new double[cols.Length];
}
}
for (int i = 0; i < cols.Length; i++)
{
double[] vals = GetColumn(cols[i], mdata);
for (int j = 0; j < include.Length; j++)
{
if (include[j])
{
rowws[j][i] = SummaryStatisticsRows.procs[j].Item2(vals);
}
}
}
List <double[]> ex = new List <double[]>();
List <string> names = new List <string>();
for (int i = 0; i < include.Length; i++)
{
if (include[i])
{
ex.Add(rowws[i]);
names.Add(SummaryStatisticsRows.procs[i].Item1);
}
}
double[,] exVals = GetExVals(ex);
string[] colNames = GetColNames(mdata, cols);
var categoryRowNames = mdata.CategoryRowNames;
var transformedCategories = TransformCategories(mdata, cols, mdata.ColumnCount);
var numericRowNames = mdata.NumericRowNames;
var transformedNumeric = TransformNumeric(mdata.NumericRows, cols, mdata.ColumnCount);
mdata.Clear();
mdata.Name = "Summary";
mdata.ColumnNames = new List <string>(names.ToArray());
mdata.ColumnDescriptions = new List <string>(names.ToArray());
mdata.Values.Set(exVals);
mdata.SetAnnotationColumns(new List <string>(new[] { "Columns" }), new List <string[]>(new[] { colNames }),
categoryRowNames, transformedCategories, numericRowNames, transformedNumeric, new List <string>(), new List <double[][]>());
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
if (string.IsNullOrWhiteSpace(remoteExe))
{
processInfo.ErrString = Resources.RemoteExeNotSpecified;
return;
}
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile, AdditionalMatrices);
var outFile = Path.GetTempFileName();
if (!TryGetCodeFile(param, out string codeFile))
{
processInfo.ErrString = $"Code file '{codeFile}' was not found";
return;
}
;
if (supplTables == null)
{
supplTables = Enumerable.Range(0, NumSupplTables).Select(i => PerseusFactory.CreateMatrixData()).ToArray();
}
var suppFiles = supplTables.Select(i => Path.GetTempFileName()).ToArray();
var commandLineArguments = GetCommandLineArguments(param);
var args = $"{codeFile} {commandLineArguments} {inFile} {outFile} {string.Join(" ", suppFiles)}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
mdata.Clear();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
for (int i = 0; i < NumSupplTables; i++)
{
PerseusUtils.ReadMatrixFromFile(supplTables[i], processInfo, suppFiles[i], '\t');
}
}
//this function is modified from PerseusPluginLib/Load/UnstructuredTxtUpload.cs LoadSplit function
//obtains the output from fdr.exe (so only applicable to PECA CORE and N)
public static void GetOutput(IMatrixData mdata, Parameters param, Parameters dataParam, string filename, string geneName, string expSeries1 = "Expression Series 1", int numOfSeries = 2)
{
char separator = '\t';
//gene name column name is not included in the file so need to replace it
//gene name
ReplaceFirstLine(filename, geneName);
string[] colNames = TabSep.GetColumnNames(filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, null, separator);
string[][] cols = TabSep.GetColumns(colNames, filename, 0, PerseusUtils.commentPrefix,
PerseusUtils.commentPrefixExceptions, separator);
int nrows = TabSep.GetRowCount(filename);
string[] expressionColumnsNames = ArrayUtils.Concat(mdata.ColumnNames, mdata.NumericColumnNames);
mdata.Clear();
mdata.Name = "PECA Analysis";
mdata.Values.Init(nrows, 0);
mdata.SetAnnotationColumns(new List <string>(colNames), new List <string>(colNames), new List <string[]>(cols), new List <string>(),
new List <string>(), new List <string[][]>(), new List <string>(), new List <string>(), new List <double[]>(),
new List <string>(), new List <string>(), new List <double[][]>());
//be careful with changes of Number of time points in the future
int numOfExpCols = numOfSeries * dataParam.GetParam <int[]>(expSeries1).Value.Length;
//file format is structured so that expressions columns are before numeric ones
//so convert the numeric ones before expression columns
//first column guaranteed to be the name column
int[] expList = Enumerable.Range(1, numOfExpCols).ToArray();
int[] numericList = Enumerable.Range(numOfExpCols + 1, colNames.Count() - numOfExpCols - 1).ToArray();
StringToNumerical(numericList, mdata);
StringToExpression(expList, mdata);
}
/// <summary>
/// An auxiliary method for testing the action of regular expressions.
/// Limited to a single column, which should be sufficient for this purpose.
/// Multiple rows are allowed to test the effect of one regex on several strings.
/// </summary>
private static void TestRegex(string regexStr, string[] stringsInit, string[] stringsExpect)
{
const string name = "Test";
IMatrixData[] supplTables = null;
IDocumentData[] documents = null;
List <string> stringColumnNames = new List <string> {
"Column Name"
};
List <string[]> stringColumnsInit = new List <string[]> {
stringsInit
};
List <string[]> stringColumnsExpect = new List <string[]> {
stringsExpect
};
Parameters param =
new Parameters(new Parameter[] {
new MultiChoiceParam("Columns", new[] { 0 })
{
Values = stringColumnNames
},
new StringParam("Regular expression", regexStr), new BoolParam("Keep original columns", false),
new BoolParam("Strings separated by semicolons are independent", false)
});
IMatrixData mdata = PerseusFactory.CreateNewMatrixData();
mdata.Clear();
mdata.Name = name;
mdata.SetAnnotationColumns(stringColumnNames, stringColumnsInit, mdata.CategoryColumnNames, new List <string[][]>(),
mdata.NumericColumnNames, mdata.NumericColumns, mdata.MultiNumericColumnNames, mdata.MultiNumericColumns);
var ptc = new ProcessTextColumns();
ptc.ProcessData(mdata, param, ref supplTables, ref documents, null);
const bool ignoreCase = false;
for (int rowInd = 0; rowInd < stringColumnsInit[0].Length; rowInd++)
{
Assert.AreEqual(mdata.StringColumns[0][rowInd], stringColumnsExpect[0][rowInd], ignoreCase);
}
}
/// <summary>
/// An auxiliary method for testing the action of regular expressions.
/// Limited to a single column, which should be sufficient for this purpose.
/// Multiple rows are allowed to test the effect of one regex on several strings.
/// </summary>
private static void TestRegex(string regexStr, string[] stringsInit, string[] stringsExpect)
{
const string name = "Test";
IMatrixData[] supplTables = null;
IDocumentData[] documents = null;
List <string> stringColumnNames = new List <string> {
"Column Name"
};
List <string[]> stringColumnsInit = new List <string[]> {
stringsInit
};
List <string[]> stringColumnsExpect = new List <string[]> {
stringsExpect
};
ProcessTextColumns ptc = new ProcessTextColumns();
IMatrixData mdata = PerseusFactory.CreateMatrixData();
mdata.Clear();
mdata.Name = name;
mdata.SetAnnotationColumns(stringColumnNames, stringColumnsInit, mdata.CategoryColumnNames, new List <string[][]>(),
mdata.NumericColumnNames, mdata.NumericColumns, mdata.MultiNumericColumnNames, mdata.MultiNumericColumns);
string errorStr = string.Empty;
Parameters param = ptc.GetParameters(mdata, ref errorStr);
param.GetParam <int[]>("Columns").Value = new[] { 0 };
param.GetParam <string>("Regular expression").Value = regexStr;
param.GetParam <bool>("Keep original columns").Value = false;
param.GetParam <bool>("Strings separated by semicolons are independent").Value = false;
ptc.ProcessData(mdata, param, ref supplTables, ref documents, null);
for (int rowInd = 0; rowInd < stringColumnsInit[0].Length; rowInd++)
{
string expected = mdata.StringColumns[0][rowInd];
string actual = stringColumnsExpect[0][rowInd];
StringAssert.AreEqualIgnoringCase(expected, actual);
}
}
public void ProcessData(IMatrixData mdata, Parameters param, ref IMatrixData[] supplTables, ref IDocumentData[] documents,
ProcessInfo processInfo)
{
var remoteExe = param.GetParam <string>(InterpreterLabel).Value;
var inFile = Path.GetTempFileName();
PerseusUtils.WriteMatrixToFile(mdata, inFile, false);
var paramFile = Path.GetTempFileName();
param.ToFile(paramFile);
var outFile = Path.GetTempFileName();
var codeFile = GetCodeFile(param);
var args = $"{codeFile} {paramFile} {inFile} {outFile}";
Debug.WriteLine($"executing > {remoteExe} {args}");
if (Utils.RunProcess(remoteExe, args, processInfo.Status, out string processInfoErrString) != 0)
{
processInfo.ErrString = processInfoErrString;
return;
}
;
mdata.Clear();
PerseusUtils.ReadMatrixFromFile(mdata, processInfo, outFile, '\t');
}
