internal static IMatrixData NonzeroFilter1Split(bool rows, int minValids, bool percentage, IMatrixData mdata,
Parameters param, double threshold, double threshold2, FilteringMode filterMode)
{
if (rows)
{
IMatrixData supplTab = (IMatrixData)mdata.Clone();
List <int> valids = new List <int>();
List <int> notvalids = new List <int>();
for (int i = 0; i < mdata.RowCount; i++)
{
int count = 0;
for (int j = 0; j < mdata.ColumnCount; j++)
{
if ((IsValid(mdata.Values.Get(i, j), threshold, threshold2, filterMode)))
{
count++;
}
}
if ((Valid(count, minValids, percentage, mdata.ColumnCount)))
{
valids.Add(i);
}
else
{
notvalids.Add(i);
}
}
// FilterRowsNew(mdata, param, valids.ToArray());
supplTab.ExtractRows(notvalids.ToArray());
return(supplTab);
}
else
{
IMatrixData supplTab = (IMatrixData)mdata.Clone();
List <int> valids = new List <int>();
List <int> notvalids = new List <int>();
for (int j = 0; j < mdata.ColumnCount; j++)
{
int count = 0;
for (int i = 0; i < mdata.RowCount; i++)
{
if (IsValid(mdata.Values.Get(i, j), threshold, threshold2, filterMode))
{
count++;
}
}
if (Valid(count, minValids, percentage, mdata.RowCount))
{
valids.Add(j);
}
else
{
notvalids.Add(j);
}
}
supplTab.ExtractColumns(notvalids.ToArray());
// FilterColumnsNew(mdata, param, valids.ToArray());
return(supplTab);
}
}
private void RemoveSelectedRowsButton_OnClick(object sender, RoutedEventArgs e)
{
int[] sel = TableView.GetSelectedRows();
if (sel.Length == 0)
{
MessageBox.Show("Please select some rows.");
}
IMatrixData mx = (IMatrixData)mdata.Clone();
mx.ExtractRows(ArrayUtils.Complement(sel, TableView.RowCount));
createNewMatrix(mx);
}
private void RemoveSelectedRowsButton_OnClick(object sender, EventArgs e)
{
int[] sel = tableView1.GetSelectedRows();
if (sel.Length == 0)
{
MessageBox.Show(Loc.PleaseSelectSomeRows);
}
IMatrixData mx = (IMatrixData)mdata.Clone();
mx.ExtractRows(ArrayUtils.Complement(sel, tableView1.RowCount));
createNewMatrix(mx);
}
public IMatrixData ProcessData(IMatrixData[] inputData, Parameters parameters, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
IMatrixData mdata1 = inputData[0];
IMatrixData mdata2 = inputData[1];
var matching = ParseMatchingColumns(parameters);
int[][] indexMap = GetIndexMap(mdata1, mdata2, matching.first, matching.second);
var result = (IMatrixData)mdata1.Clone();
result.Origin = "Combination";
var addIndicator = parameters.GetParam <bool>("Add indicator").Value;
if (addIndicator)
{
AddIndicator(result, mdata2, indexMap);
}
var(main, text, numeric, category) = ParseCopyParameters(parameters);
SetAnnotationRows(result, mdata1, mdata2, main.copy);
AddMainColumns(result, mdata2, indexMap, main.copy, GetAveraging(main.combine));
AddAnnotationColumns(result, mdata2, indexMap, text, numeric, category);
return(result);
}
public static int WriteRNAFiles(IMatrixData mdata, Parameters param, Parameters dataParam, string workingDirectory, out string errString, string RNAexp)
{
//need to write a general version
//accepts text only data for now
string fileTempY = System.IO.Path.Combine(workingDirectory, @".\tempY.txt");
string fileY = System.IO.Path.Combine(workingDirectory, @".\fileY.txt");
IMatrixData mCopyY = (IMatrixData)mdata.Clone();
int[] nameInd = new[] { param.GetParam <int>("Gene Name Column").Value };
int[] yInd = dataParam.GetParam <int[]>(RNAexp).Value;
double baseVal = GetBase(dataParam.GetParamWithSubParams <int>(PECAParameters.dataFormGeneric));
SetupMDataForInput(mCopyY, yInd, nameInd, baseVal);
try
{
//hacky way of removing comments
PerseusUtils.WriteMatrixToFile(mCopyY, fileTempY, false);
RemoveCommentsFromFile(fileTempY, fileY);
}
catch (Exception e)
{
//need to reorganize this
errString = e.ToString();
return(-1);
}
errString = null;
return(0);
}
public static IMatrixData CreateSupplTabSplitValids(IMatrixData mdata, int[] rows)
{
IMatrixData supplTab = (IMatrixData)mdata.Clone();
supplTab.ExtractRows(rows);
return(supplTab);
}
public IMatrixData ProcessData(IMatrixData[] inputData, Parameters parameters, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
IMatrixData mdata1 = inputData[0];
Dictionary <string, string> map = GetMap(inputData[1], parameters);
IMatrixData result = (IMatrixData)mdata1.Clone();
int ind = parameters.GetParam <int>("Column in matrix 1 to be edited").Value;
string[] x = mdata1.StringColumns[ind];
for (int i = 0; i < x.Length; i++)
{
x[i] = Process(x[i], map);
}
return(result);
}
public IMatrixData ProcessData(IMatrixData[] inputData, Parameters parameters, ref IMatrixData[] supplTables,
ref IDocumentData[] documents, ProcessInfo processInfo)
{
IMatrixData mdata1 = inputData[0];
IMatrixData mdata2 = inputData[1];
((int, int)first, (int, int)? second, bool outer, bool ignoreCase)matching =
ParseMatchingColumns(parameters);
(int[][] indexMap, int[] unmappedRightIndices) =
GetIndexMap(mdata1, mdata2, matching.first, matching.second, matching.ignoreCase);
IMatrixData result = (IMatrixData)mdata1.Clone();
result.Origin = "Combination";
if (matching.outer)
{
int[][] extendedIndexMap = new int[indexMap.Length + unmappedRightIndices.Length][];
Array.Copy(indexMap, extendedIndexMap, indexMap.Length);
for (int i = 0; i < unmappedRightIndices.Length; i++)
{
int idx = indexMap.Length + i;
extendedIndexMap[idx] = new[] { unmappedRightIndices[i] };
}
result.AddEmptyRows(unmappedRightIndices.Length);
UpdateIdColumns(result, mdata2, indexMap.Length, unmappedRightIndices, matching.first, matching.second);
indexMap = extendedIndexMap;
}
bool addIndicator = parameters.GetParam <bool>("Add indicator").Value;
if (addIndicator)
{
AddIndicator(result, mdata2, indexMap);
}
bool addRowIndex = parameters.GetParam <bool>("Add original row numbers").Value;
if (addRowIndex)
{
result.AddMultiNumericColumn("Original row numbers", "",
indexMap.Select(rows => rows.Select(Convert.ToDouble).ToArray()).ToArray());
}
((int[] copy, int combine)main, int[] text, (int[] copy, int combine)numeric, int[] category) =
ParseCopyParameters(parameters);
SetAnnotationRows(result, mdata1, mdata2, main.copy);
AddMainColumns(result, mdata2, indexMap, main.copy, GetAveraging(main.combine));
AddAnnotationColumns(result, mdata2, indexMap, text, numeric, category);
return(result);
}
private static IMatrixData GetResult(IMatrixData mdata1, IMatrixData mdata2,
Parameters parameters, IList <int[]> indexMap)
{
IMatrixData result = (IMatrixData)mdata1.Clone();
SetAnnotationRows(result, mdata1, mdata2);
bool indicator = parameters.GetParam <bool>("Indicator").Value;
if (indicator)
{
string[][] indicatorCol = new string[indexMap.Count][];
for (int i = 0; i < indexMap.Count; i++)
{
indicatorCol[i] = indexMap[i].Length > 0 ? new[] { "+" } : new string[0];
}
result.AddCategoryColumn(mdata2.Name, "", indicatorCol);
}
result.Origin = "Combination";
return(result);
}
public static int WriteInputFiles(IMatrixData mdata, Parameters param, string workingDirectory, out string errString, string expSeries1 = "Expression Series 1", string expSeries2 = "Expression Series 2", string expSeries3 = "Expression Series 3")
{
//need to write a general version
//accepts text only data for now
//set as global
string fileTempX = System.IO.Path.Combine(workingDirectory, @".\tempX.txt");
string fileX = System.IO.Path.Combine(workingDirectory, @".\fileX.txt");
string fileTempM = System.IO.Path.Combine(workingDirectory, @".\tempM.txt");
string fileM = System.IO.Path.Combine(workingDirectory, @".\fileM.txt");
string fileTempY = System.IO.Path.Combine(workingDirectory, @".\tempY.txt");
string fileY = System.IO.Path.Combine(workingDirectory, @".\fileY.txt");
IMatrixData mCopyX = (IMatrixData)mdata.Clone();
IMatrixData mCopyM = (IMatrixData)mdata.Clone();
IMatrixData mCopyY = (IMatrixData)mdata.Clone();
int[] nameInd = new[] { param.GetParam <int>("Gene Name Column").Value };
int[] xInd = param.GetParam <int[]>(expSeries1).Value;
int[] mInd = param.GetParam <int[]>(expSeries2).Value;
int[] yInd = param.GetParam <int[]>(expSeries3).Value;
//int n_tp = param.GetParam<int>("Number of Time Points").Value;
int n_rep = param.GetParam <int>("Number of Replicates").Value;
if (nameInd.Length == 0)
{
errString = "Please select a gene name column";
return(-1);
}
if (xInd.Length == 0)
{
errString = "Please select some columns for Expression Series";
return(-1);
}
if (xInd.Length != yInd.Length || xInd.Length != mInd.Length)
{
errString = "Expression Series need to have matching number of columns";
return(-1);
}
if ((xInd.Length % n_rep) != 0)
{
errString = "number of columns not multiple of Number of Replicates";
return(-1);
}
//check also timepoints here
//if ((xInd.Length % n_tp)!=0)
//{
// errString = "number of columns not multiple of Number of Time Points";
// return -1;
//}
double baseVal1 = PluginPECA.Utils.GetBase(param.GetParamWithSubParams <int>(PECAParameters.dataForm1));
double baseVal2 = PluginPECA.Utils.GetBase(param.GetParamWithSubParams <int>(PECAParameters.dataForm2));
double baseVal3 = PluginPECA.Utils.GetBase(param.GetParamWithSubParams <int>(PECAParameters.dataForm3));
PluginPECA.Utils.SetupMDataForInput(mCopyX, xInd, nameInd, baseVal1);
PluginPECA.Utils.SetupMDataForInput(mCopyM, mInd, nameInd, baseVal2);
PluginPECA.Utils.SetupMDataForInput(mCopyY, yInd, nameInd, baseVal3);
try
{
//hacky way of removing comments
//better to just ask GS to ignore comments from his code
PerseusUtils.WriteMatrixToFile(mCopyX, fileTempX, false);
PluginPECA.Utils.RemoveCommentsFromFile(fileTempX, fileX);
PerseusUtils.WriteMatrixToFile(mCopyM, fileTempM, false);
PluginPECA.Utils.RemoveCommentsFromFile(fileTempM, fileM);
PerseusUtils.WriteMatrixToFile(mCopyY, fileTempY, false);
PluginPECA.Utils.RemoveCommentsFromFile(fileTempY, fileY);
}
catch (Exception e)
{
//need to reorganize this
errString = e.ToString();
return(-1);
}
errString = null;
return(0);
}
public static IMatrixData CreateSupplTab(IMatrixData mdata)
{
IMatrixData supplTab = (IMatrixData)mdata.Clone();
return(supplTab);
}
