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GinRibbon_old.cs
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GinRibbon_old.cs
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#undef CLICK_CHART // check to include clickable chart and events.. only if object storage is an option.
using Microsoft.Office.Tools.Ribbon;
using System;
using System.Collections.Generic;
using System.Collections.Specialized;
using System.Data;
using System.Drawing.Imaging;
using System.Linq;
using System.Windows.Forms;
using Excel = Microsoft.Office.Interop.Excel;
using SysData = System.Data;
namespace GINtool
{
public partial class GinRibbon
{
#region inits
bool gOperonOutput = false;
bool gCatOutput = false;
//bool gpValueUpdate = true;
//bool gRegulonPlot = true;
#if CLICK_CHART
List<chart_info> gCharts = new List<chart_info>();
#endif
byte gNeedsUpdate = (byte)UPDATE_FLAGS.ALL;
List<TASKS> gTasks = new List<TASKS>();
// int[] updateFlags = new int[3] { 1, 1, 1 };
//bool SummaryTableNeedsUpdating = true;
//bool CombinedTableNeedsUpdating = true;
//bool OperonTableNeedsUpdating = true;
//bool MappedTableNeedsUpdating = true;
//bool RegulonPlotsNeedsUpdating = true;
//bool CategoryPlotNeedsUpdating = true;
//bool DistributionPlotNeedsUpdating = true;
//bool RegulonPlotNeedsUpdating = true;
int maxGenesPerOperon = 1;
SysData.DataTable gRefWB = null; // RegulonData .. rename later
SysData.DataTable gRefStats = null;
SysData.DataTable gRefOperons = null;
SysData.DataTable gCategories = null;
string[] gColNames = null;
string gCategoryGeneColumn = "locus_tag"; // the fixed column name that refers to the genes inthe category csv file
Excel.Application gApplication = null;
//bool gGeneratePlots = false;
//bool gQPlot = false;
//bool gNeedsUpdating = true;
//bool gOrderAscending = true;
bool gSortResults = false;
//bool gUseCatOutput = false;
static List<string> gAvailItems = null;
static List<string> gUpItems = null;
static List<string> gDownItems = null;
List<int> gExcelErrorValues = null;
string gInputRange = "";
List<FC_BSU> gOutput = null;
SysData.DataTable gSummary = null;
List<BsuRegulons> gList = null;
SysData.DataTable gCombineInfo = null;
//int gDDcatLevel = 1;
// private bool gPlotDistribution = false;
// private bool gPlotClustered = false; // is category plot
//PlotRoutines gEnrichmentAnalysis;
#endregion
#region database_utils
private List<string> propertyItems(string property)
{
StringCollection myCol = (StringCollection)Properties.Settings.Default[property];
if (myCol != null)
return myCol.Cast<string>().ToList();
return new List<string>();
}
private void storeValue(string property, List<string> aValue)
{
StringCollection collection = new StringCollection();
collection.AddRange(aValue.ToArray());
Properties.Settings.Default[property] = collection;
}
private SysData.DataTable GetDistinctRecords(SysData.DataTable dt, string[] Columns)
{
return dt.DefaultView.ToTable(true, Columns);
}
private SysData.DataRow[] Lookup(string value)
{
SysData.DataRow[] filteredRows = gRefWB.Select(string.Format("[{0}] LIKE '%{1}%'", Properties.Settings.Default.referenceBSU, value));
// copy data to temporary table
SysData.DataTable dt = gRefWB.Clone();
foreach (SysData.DataRow dr in filteredRows)
dt.ImportRow(dr);
// return only unique values
SysData.DataTable dt_unique = GetDistinctRecords(dt, gColNames);
return dt_unique.Select();
}
#endregion
private bool LoadCategoryData()
{
if (Properties.Settings.Default.categoryFile.Length == 0 || Properties.Settings.Default.catSheet.Length == 0)
return false;
//gApplication.StatusBar = "Load category data";
//gApplication.EnableEvents = false;
AddTask(TASKS.LOAD_CATEGORY_DATA);
SysData.DataTable _tmp = ExcelUtils.ReadExcelToDatable(gApplication, Properties.Settings.Default.catSheet, Properties.Settings.Default.categoryFile, 1, 1);
gCategories = new SysData.DataTable("Categories");
gCategories.CaseSensitive = false;
gCategories.Columns.Add("catid", Type.GetType("System.String"));
gCategories.Columns.Add("catid_short", Type.GetType("System.String"));
gCategories.Columns.Add("gene", Type.GetType("System.String"));
gCategories.Columns.Add("locus_tag", Type.GetType("System.String"));
gCategories.Columns.Add("cat1", Type.GetType("System.String"));
gCategories.Columns.Add("cat2", Type.GetType("System.String"));
gCategories.Columns.Add("cat3", Type.GetType("System.String"));
gCategories.Columns.Add("cat4", Type.GetType("System.String"));
gCategories.Columns.Add("cat5", Type.GetType("System.String"));
gCategories.Columns.Add("cat1_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("cat2_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("cat3_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("cat4_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("cat5_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("ucat1_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("ucat2_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("ucat3_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("ucat4_int", Type.GetType("System.Int32"));
gCategories.Columns.Add("ucat5_int", Type.GetType("System.Int32"));
string[] lcols = new string [] {"cat1_int","cat2_int","cat3_int","cat4_int","cat5_int"};
string[] ulcols = new string[] { "ucat1_int", "ucat2_int", "ucat3_int", "ucat4_int", "ucat5_int" };
foreach (SysData.DataRow lRow in _tmp.Rows)
{
object[] lItems = lRow.ItemArray;
SysData.DataRow lNewRow = gCategories.Rows.Add();
for (int i = 0; i < lItems.Length; i++)
{
lNewRow["catid"] = lItems[0];
string[] splits = lItems[0].ToString().Split(' ');
lNewRow["catid_short"] = splits[splits.Count()-1];
lNewRow["Gene"] = lItems[1];
lNewRow["locus_tag"] = lItems[2];
lNewRow["cat1"] = lItems[3];
lNewRow["cat2"] = lItems[4];
lNewRow["cat3"] = lItems[5];
lNewRow["cat4"] = lItems[6];
lNewRow["cat5"] = lItems[7];
string[] llItems = lItems[0].ToString().Split(' ')[1].Split('.');
for (int j = 0; j < llItems.Length; j++)
{
lNewRow[lcols[j]] = Int32.Parse(llItems[j]);
}
for (int j = llItems.Length; j < 5; j++)
{
//lNewRow[lcols[j]] = 0;
//lNewRow[ulcols[j]] = 0;
}
int offset = 0;
for (int j = 0; j < llItems.Length; j++)
{
lNewRow[ulcols[j]] = offset + ((Int32)lNewRow[lcols[j]]) * Math.Pow(10, 5 - j);
offset = (Int32)lNewRow[ulcols[j]];
}
}
}
//gApplication.EnableEvents = true;
//gApplication.StatusBar = "Ready";
RemoveTask(TASKS.LOAD_CATEGORY_DATA);
return gCategories.Rows.Count > 0;
}
private bool LoadOperonData()
{
if (Properties.Settings.Default.operonFile.Length == 0 || Properties.Settings.Default.operonSheet.Length == 0)
return false;
AddTask(TASKS.LOAD_OPERON_DATA);
//gApplication.EnableEvents = false;
//gApplication.StatusBar = "Load operon data";
SysData.DataTable _tmp = ExcelUtils.ReadExcelToDatable(gApplication, Properties.Settings.Default.operonSheet, Properties.Settings.Default.operonFile, 1, 1);
gRefOperons = new SysData.DataTable("OPERONS");
gRefOperons.CaseSensitive = false;
gRefOperons.Columns.Add("operon", Type.GetType("System.String"));
gRefOperons.Columns.Add("gene", Type.GetType("System.String"));
foreach(SysData.DataRow lRow in _tmp.Rows)
{
string[] lItems = lRow.ItemArray[0].ToString().Split('-');
if (maxGenesPerOperon < lItems.Length)
maxGenesPerOperon = lItems.Length;
for (int i = 0; i < lItems.Length; i++)
{
SysData.DataRow lNewRow = gRefOperons.Rows.Add();
lNewRow["operon"] = lItems[0];
lNewRow["gene"] = lItems[i];
}
}
//gApplication.EnableEvents = true;
//gApplication.StatusBar = "Ready";
RemoveTask(TASKS.LOAD_OPERON_DATA);
return gRefOperons.Rows.Count>0;
}
private bool LoadData()
{
//gApplication.StatusBar = "Load regulon/gene mappings";
//gApplication.EnableEvents = false;
AddTask(TASKS.LOAD_REGULON_DATA);
gRefWB = ExcelUtils.ReadExcelToDatable(gApplication, Properties.Settings.Default.referenceSheetName, Properties.Settings.Default.referenceFile, 1, 1);
if (gRefWB != null)
{
gColNames = new string[gRefWB.Columns.Count];
int i = 0;
foreach (SysData.DataColumn col in gRefWB.Columns)
{
gColNames[i++] = col.ColumnName;
}
// generate database frequency table
CreateTableStatistics();
}
//gApplication.EnableEvents = true;
//gApplication.StatusBar = "Ready";
RemoveTask(TASKS.LOAD_REGULON_DATA);
return gRefWB != null ? true : false;
}
private void CreateTableStatistics()
{
List<string> lString = new List<string> { Properties.Settings.Default.referenceRegulon };
SysData.DataTable lUnique = GetDistinctRecords(gRefWB, lString.ToArray());
// initialize the global datatable
gRefStats = new SysData.DataTable("tblstat");
int totNrRows = gRefWB.Rows.Count;
SysData.DataColumn regColumn = new SysData.DataColumn("Regulon", Type.GetType("System.String"));
SysData.DataColumn countColumn = new SysData.DataColumn("Count", Type.GetType("System.Int16"));
SysData.DataColumn avgColumn = new SysData.DataColumn("Average", Type.GetType("System.Double"));
gRefStats.Columns.Add(regColumn);
gRefStats.Columns.Add(countColumn);
gRefStats.Columns.Add(avgColumn);
foreach (SysData.DataRow lRow in lUnique.Rows)
{
string lVal = lRow[Properties.Settings.Default.referenceRegulon].ToString();
int cnt = gRefWB.Select(string.Format("{0}='{1}'", Properties.Settings.Default.referenceRegulon, lVal)).Length;
SysData.DataRow nRow = gRefStats.Rows.Add();
nRow["Regulon"] = lVal;
nRow["Count"] = cnt;
nRow["Average"] = ((double)cnt) / totNrRows;
}
}
private void GinRibbon_Load(object sender, RibbonUIEventArgs e)
{
gApplication = Globals.ThisAddIn.GetExcelApplication();
btnRegulonFileName.Label = Properties.Settings.Default.referenceFile;
btnOperonFile.Label = Properties.Settings.Default.operonFile;
btnCatFile.Label = Properties.Settings.Default.categoryFile;
cbOrderFC.Checked = Properties.Settings.Default.useSort;
cbDescending.Checked = !Properties.Settings.Default.sortAscending;
cbAscending.Checked = Properties.Settings.Default.sortAscending;
chkRegulon.Checked = Properties.Settings.Default.regPlot;
cbMapping.Checked = Properties.Settings.Default.tblMap;
cbSummary.Checked = Properties.Settings.Default.tblSummary;
cbCombined.Checked = Properties.Settings.Default.tblCombine;
cbOperon.Checked = Properties.Settings.Default.tblOperon;
cbClustered.Checked = Properties.Settings.Default.catPlot;
cbDistribution.Checked = Properties.Settings.Default.distPlot;
//chkRegulon.Checked = Properties.Settings.Default.regPlot;
//cbOrderFC.Checked = Properties.Settings.Default.useFCorder;
cbUseCategories.Checked = Properties.Settings.Default.useCat;
cbUsePValues.Checked = Properties.Settings.Default.use_pvalues;
cbUseFoldChanges.Checked = !Properties.Settings.Default.use_pvalues;
if (Properties.Settings.Default.operonFile.Length == 0)
btnOperonFile.Label = "No file selected";
gAvailItems = propertyItems("directionMapUnassigned");
gUpItems = propertyItems("directionMapUp");
gDownItems = propertyItems("directionMapDown");
btnSelect.Enabled = false;
btApply.Enabled = false;
ddBSU.Enabled = false;
ddGene.Enabled = false;
ddRegulon.Enabled = false;
ddDir.Enabled = false;
btPlot.Enabled = false;
cbUseCategories.Enabled = false;
cbMapping.Enabled = false;
cbSummary.Enabled = false;
cbCombined.Enabled = false;
cbOperon.Enabled = false;
cbOrderFC.Enabled = false;
cbUsePValues.Enabled = false;
cbUseFoldChanges.Enabled = false;
toggleButton1.Enabled = true;
cbAscending.Enabled = false;
cbDescending.Enabled = false;
//grpDirection.Visible = false;
//gOrderAscending = cbOrderFC.Checked;
//edtMaxGroups.Enabled = false;
//btnPalette.Enabled = false;
//cbGenPlots.Checked = Properties.Settings.Default.generatePlots;
//cbQplot.Checked = Properties.Settings.Default.qPlot;
//gCompositPlot = cbGenPlots.Checked;
//gQPlot = cbQplot.Enabled;
//if (cbGenPlots.Checked )
//if (gEnrichmentAnalysis == null)
//{
// gEnrichmentAnalysis = new PlotRoutines(gApplication);
//}
PlotRoutines.theApp = gApplication;
EnableOutputOptions(false);
gExcelErrorValues = ((int[])Enum.GetValues(typeof(ExcelUtils.CVErrEnum))).ToList();
//if (Properties.Settings.Default.use_pvalues)
//{
// splitButton3.Label = but_pvalues.Label;
// splitButton3.Image = but_pvalues.Image;
//}
//else
//{
// splitButton3.Label = but_fc.Label;
// splitButton3.Image = but_pvalues.Image;
//}
btLoad.Enabled = System.IO.File.Exists(Properties.Settings.Default.referenceFile);
}
private Excel.Range GetActiveCell()
{
if (gApplication != null)
{
try { return (Excel.Range)gApplication.Selection; }
catch (Exception e) { return null; }
}
return null;
}
private void EnableOutputOptions(bool enable)
{
ebLow.Enabled = enable;
ebMid.Enabled = enable;
ebHigh.Enabled = enable;
editMinPval.Enabled = enable;
//splitButton3.Enabled = enable;
//cbUseCategories.Enabled = enable;
cbMapping.Enabled = enable;
cbSummary.Enabled = enable;
cbCombined.Enabled = enable;
cbClustered.Enabled = enable;
cbDistribution.Enabled = enable;
chkRegulon.Enabled= enable;
cbOrderFC.Enabled = enable;
cbUseCategories.Enabled = enable && gCatOutput;
cbOperon.Enabled = enable && gOperonOutput;
cbUsePValues.Enabled = enable;
cbUseFoldChanges.Enabled = enable;
cbAscending.Enabled = enable;
cbDescending.Enabled = enable;
//splitbtnEA.Enabled = enable;
}
private Excel.Worksheet GetActiveSheet()
{
if (gApplication != null)
{
if (gApplication.ActiveSheet is Excel.Chart)
{
MessageBox.Show("Please activate data sheet and select columns with data");
return null;
}
try
{
return (Excel.Worksheet)gApplication.ActiveSheet;
}
catch(Exception ex)
{
MessageBox.Show(ex.Message.ToString());
}
}
return null;
}
private void ConditionFormatRange(Excel.Range columnRange)
{
Excel.FormatConditions fcs = columnRange.FormatConditions;
var formatCondition = fcs.Add(Microsoft.Office.Interop.Excel.XlFormatConditionType.xlDatabar);
formatCondition.MinPoint.Modify(Microsoft.Office.Interop.Excel.XlConditionValueTypes.xlConditionValueAutomaticMin);
formatCondition.MaxPoint.Modify(Microsoft.Office.Interop.Excel.XlConditionValueTypes.xlConditionValueAutomaticMax);
formatCondition.BarFillType = Microsoft.Office.Interop.Excel.XlGradientFillType.xlGradientFillPath;
formatCondition.Direction = Microsoft.Office.Interop.Excel.Constants.xlContext;
formatCondition.NegativeBarFormat.ColorType = Microsoft.Office.Interop.Excel.XlDataBarNegativeColorType.xlDataBarColor;
formatCondition.BarColor.Color = 8700771; // System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightGreen);
formatCondition.BarColor.TintAndShade = 0; // System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightGreen);
formatCondition.BarBorder.Color.Color = 8700771; // System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightGreen);
formatCondition.BarBorder.Type = Microsoft.Office.Interop.Excel.XlDataBarBorderType.xlDataBarBorderSolid;
formatCondition.NegativeBarFormat.BorderColorType = Microsoft.Office.Interop.Excel.XlDataBarNegativeColorType.xlDataBarColor;
formatCondition.NegativeBarFormat.Parent.BarBorder.Type = Microsoft.Office.Interop.Excel.XlDataBarBorderType.xlDataBarBorderSolid;
formatCondition.AxisPosition = Microsoft.Office.Interop.Excel.XlDataBarAxisPosition.xlDataBarAxisAutomatic;
formatCondition.AxisColor.Color = 0; // System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.White);
formatCondition.AxisColor.TintAndShade = 0;
formatCondition.NegativeBarFormat.Color.Color = 255; // System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightSalmon);
formatCondition.NegativeBarFormat.Color.TintAndShade = 0;
formatCondition.NegativeBarFormat.BorderColor.Color = 255; // System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightSalmon);
formatCondition.NegativeBarFormat.BorderColor.TintAndShade = 0;
}
private bool iserrorCell(object obj)
{
return (obj is Int32) && gExcelErrorValues.Contains((Int32)obj);
}
private List<BsuRegulons> QueryResultTable(Excel.Range theCells)
{
AddTask(TASKS.MAPPING_GENES_TO_REGULONS);
List<BsuRegulons> lList = new List<BsuRegulons>();
foreach (Excel.Range c in theCells.Rows)
{
string lBSU;
double lFC = 0;
double lPvalue = 1;
BsuRegulons lMap = null;
if (c.Columns.Count == 3)
{
object[,] value = c.Value2;
// first check if the cell contains an erroneous value, if not then try to parse the value or reset to default
if (!iserrorCell(value[1, 1]))
if (!Double.TryParse(value[1, 1].ToString(), out lPvalue))
lPvalue = 1;
if (!iserrorCell(value[1, 2]))
if (!Double.TryParse(value[1, 2].ToString(), out lFC))
lFC = 0;
lBSU = value[1, 3].ToString();
lMap = new BsuRegulons(lFC, lPvalue, lBSU);
}
if (lMap.BSU.Length > 0)
{
SysData.DataRow[] results = Lookup(lMap.BSU);
if (results.Length > 0)
{
string gene = results[0][Properties.Settings.Default.referenceGene].ToString();
lMap.GENE = gene;
for (int r = 0; r < results.Length; r++)
{
string item = results[r][Properties.Settings.Default.referenceRegulon].ToString();
string direction = results[r][Properties.Settings.Default.referenceDIR].ToString();
if (item.Length > 0) // loop over found regulons
{
lMap.REGULONS.Add(item);
if (gUpItems.Contains(direction))
lMap.UP.Add(r);
if (gDownItems.Contains(direction))
lMap.DOWN.Add(r);
}
}
}
}
lList.Add(lMap);
}
RemoveTask(TASKS.MAPPING_GENES_TO_REGULONS);
return lList;
}
(SysData.DataTable, SysData.DataTable) PrepareResultTable(List<BsuRegulons> lResults)
{
SysData.DataTable myTable = new System.Data.DataTable("mytable");
SysData.DataTable clrTable = new System.Data.DataTable("colortable");
int maxcol = lResults[0].REGULONS.Count;
// count max number of columns neccesary
for (int r = 1; r < lResults.Count; r++)
if (maxcol < lResults[r].REGULONS.Count)
maxcol = lResults[r].REGULONS.Count;
// add BSU/gene/p-value/fc columns
SysData.DataColumn bsuCol = new SysData.DataColumn("bsu", Type.GetType("System.String"));
myTable.Columns.Add(bsuCol);
SysData.DataColumn geneCol = new SysData.DataColumn("gene", Type.GetType("System.String"));
myTable.Columns.Add(geneCol);
SysData.DataColumn fcCol = new SysData.DataColumn("fc", Type.GetType("System.Double"));
myTable.Columns.Add(fcCol);
SysData.DataColumn pValCol = new SysData.DataColumn("pval", Type.GetType("System.Double"));
myTable.Columns.Add(pValCol);
// add count column
SysData.DataColumn countCol = new SysData.DataColumn("count_col", Type.GetType("System.Int16"));
myTable.Columns.Add(countCol);
// add variable columns
for (int c = 0; c < maxcol; c++)
{
SysData.DataColumn newCol = new SysData.DataColumn(string.Format("col_{0}", c + 1));
myTable.Columns.Add(newCol);
SysData.DataColumn clrCol = new SysData.DataColumn(string.Format("col_{0}", c + 1), Type.GetType("System.Int16"));
clrTable.Columns.Add(clrCol);
}
// fill data
for (int r = 0; r < lResults.Count; r++)
{
SysData.DataRow newRow = myTable.Rows.Add();
newRow["bsu"] = lResults[r].BSU;
newRow["gene"] = lResults[r].GENE;
newRow["fc"] = lResults[r].FC;
newRow["pval"] = lResults[r].PVALUE;
newRow["count_col"] = lResults[r].TOT;
SysData.DataRow clrRow = clrTable.Rows.Add();
for (int c = 0; c < lResults[r].REGULONS.Count; c++)
newRow[string.Format("col_{0}", c + 1)] = lResults[r].REGULONS[c];
for (int c = 0; c < lResults[r].UP.Count; c++)
clrRow[lResults[r].UP[c]] = 1;
for (int c = 0; c < lResults[r].DOWN.Count; c++)
clrRow[lResults[r].DOWN[c]] = -1;
}
return (myTable, clrTable);
}
public string RangeAddress(Excel.Range rng)
{
return rng.get_AddressLocal(false, false, Excel.XlReferenceStyle.xlA1,Type.Missing, Type.Missing);
}
public string CellAddress(Excel.Worksheet sht, int row, int col)
{
return RangeAddress(sht.Cells[row, col]);
}
private string GetStatusTask(TASKS task)
{
return taks_strings[(int)task];
}
private void SetStatus(TASKS activeTask)
{
gApplication.StatusBar = GetStatusTask(activeTask);
if (activeTask != TASKS.READY)
{
gApplication.ScreenUpdating = false;
gApplication.DisplayAlerts = false;
gApplication.EnableEvents = false;
}
else
{
gApplication.ScreenUpdating = true;
gApplication.DisplayAlerts = true;
gApplication.EnableEvents = true;
}
}
private void AddTask(TASKS newTask)
{
gTasks.Add(newTask);
SetStatus(newTask);
}
private void RemoveTask(TASKS taskReady)
{
gTasks.Remove(taskReady);
if (gTasks.Count == 0 || gTasks[0] == TASKS.READY)
SetStatus(TASKS.READY);
else
SetStatus(gTasks.Last());
}
// the main routine after mouse selection update // generates mapping output.. should be de-coupled (update data & mapping output)
private (List<FC_BSU>, List<BsuRegulons>) GenerateOutput(bool suppressOutput=false)
{
AddTask(TASKS.READ_SHEET_DATA);
Excel.Range theInputCells = GetActiveCell();
Excel.Worksheet theSheet = GetActiveSheet();
if (theSheet == null)
{
MessageBox.Show("Please select a worksheet with data first");
RemoveTask(TASKS.READ_SHEET_DATA);
return (null, null);
}
if (theSheet.Name.Contains("Plot_") || theSheet.Name.Contains("CongruenceData_") || theSheet.Name.Contains("CongruencePlot_") || theSheet.Name.Contains("Summary_") ||
theSheet.Name.Contains("Combined_") || theSheet.Name.Contains("Mapped_") || theInputCells.Columns.Count != 3 )
{
MessageBox.Show("Please select 3 columns (first P-Value, second FC, third BSU)");
RemoveTask(TASKS.READ_SHEET_DATA);
return (null, null);
}
if (RangeAddress(theInputCells) != gInputRange || (gOutput == null || gList == null))
{
gInputRange = RangeAddress(theInputCells);
gNeedsUpdate = (byte)UPDATE_FLAGS.ALL;
}
else
{
RemoveTask(TASKS.READ_SHEET_DATA);
return (gOutput, gList);
}
int nrRows = theInputCells.Rows.Count;
int startC = theInputCells.Column;
int startR = theInputCells.Row;
// from now always assume 3 columns.. p-value, fc, bsu
// generate the results for outputting the data and summary
List<BsuRegulons> lResults = QueryResultTable(theInputCells);
List<FC_BSU> lOutput = new List<FC_BSU>();
for (int r = 0; r < nrRows; r++)
for (int c = 0; c < lResults[r].REGULONS.Count; c++)
{
int val = 0;
if (lResults[r].UP.Contains(c))
val = 1;
if (lResults[r].DOWN.Contains(c))
val = -1;
lOutput.Add(new FC_BSU(lResults[r].FC, lResults[r].REGULONS[c], val, lResults[r].PVALUE,lResults[r].GENE));
}
RemoveTask(TASKS.READ_SHEET_DATA);
return (lOutput, lResults);
}
private void CreateMappingSheet(List<BsuRegulons> bsuRegulons)
{
var lOut = PrepareResultTable(bsuRegulons);
SysData.DataTable lTable = lOut.Item1;
SysData.DataTable clrTbl;
AddTask(TASKS.UPDATE_MAPPED_TABLE);
//gApplication.StatusBar = "Creating mapping sheet";
int nrRows = lTable.Rows.Count;
//int startC = 1;
int startR = 2;
// from now always assume 3 columns.. p-value, fc, bsu
int offsetColumn = 1;
Excel.Worksheet lNewSheet = gApplication.Worksheets.Add();
renameWorksheet(lNewSheet, "Mapped_");
lNewSheet.Cells[1, 1] = "BSU";
lNewSheet.Cells[1, 2] = "GENE";
lNewSheet.Cells[1, 3] = "FC";
lNewSheet.Cells[1, 4] = "PVALUE";
lNewSheet.Cells[1, 5] = "TOT REGULONS";
string lastColumn = lTable.Columns[lTable.Columns.Count - 1].ColumnName;
lastColumn = lastColumn.Replace("col_", "");
int maxreg = Int16.Parse(lastColumn);
for (int i = 0; i < maxreg; i++)
lNewSheet.Cells[1, i + 6] = string.Format("Regulon_{0}", i + 1);
FastDtToExcel(lTable, lNewSheet, startR, offsetColumn, startR + nrRows - 1, offsetColumn + lTable.Columns.Count - 1);
Excel.Range top = lNewSheet.Cells[1, 1];
Excel.Range bottom = lNewSheet.Cells[lTable.Rows.Count + 1, lTable.Columns.Count];
Excel.Range all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Columns.AutoFit();
clrTbl = lOut.Item2;
ColorCells(clrTbl, lNewSheet, startR, offsetColumn + 5, startR + nrRows - 1, offsetColumn + lTable.Columns.Count - 1);
RemoveTask(TASKS.UPDATE_MAPPED_TABLE);
}
private void FastDtToExcel(System.Data.DataTable dt, Excel.Worksheet sheet, int firstRow, int firstCol, int lastRow, int lastCol)
{
Excel.Range top = sheet.Cells[firstRow, firstCol];
Excel.Range bottom = sheet.Cells[lastRow, lastCol];
Excel.Range all = (Excel.Range)sheet.get_Range(top, bottom);
object[,] arrayDT = new object[dt.Rows.Count, dt.Columns.Count];
for (int i = 0; i < dt.Rows.Count; i++)
for (int j = 0; j < dt.Columns.Count; j++)
arrayDT[i, j] = dt.Rows[i][j];
all.Value = arrayDT;
}
private void ColorCells(System.Data.DataTable dt, Excel.Worksheet sheet, int firstRow, int firstCol, int lastRow, int lastCol)
{
AddTask(TASKS.COLOR_CELLS);
Excel.Range top = sheet.Cells[firstRow, firstCol];
Excel.Range bottom = sheet.Cells[lastRow, lastCol];
Excel.Range all = (Excel.Range)sheet.get_Range(top, bottom);
for (int r = 0; r < dt.Rows.Count; r++)
{
SysData.DataRow clrRow = dt.Rows[r];
for (int c = 0; c < clrRow.ItemArray.Length; c++)
{
Excel.Range lR = all.Cells[r + 1, c + 1];
if (Int32.TryParse(clrRow[c].ToString(), out int val))
{
if (val == 1)
lR.Interior.Color = System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightGreen);
if (val == -1)
lR.Interior.Color = System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightSalmon);
}
}
}
RemoveTask(TASKS.COLOR_CELLS);
}
private void CreateSummarySheet(SysData.DataTable theTable)
{
AddTask(TASKS.UPDATE_SUMMARY_TABLE);
Excel.Worksheet lNewSheet = gApplication.Worksheets.Add();
renameWorksheet(lNewSheet, "Summary_");
int col = 1;
Excel.Range top = lNewSheet.Cells[1, 4];
Excel.Range bottom = lNewSheet.Cells[1, 11];
Excel.Range all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Merge();
all.Value = "Observed Counts and directions";
all.HorizontalAlignment = Microsoft.Office.Interop.Excel.Constants.xlCenter;
top = lNewSheet.Cells[1, 13];
bottom = lNewSheet.Cells[1, 20];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Merge();
all.Value = "Percentage";
all.HorizontalAlignment = Microsoft.Office.Interop.Excel.Constants.xlCenter;
top = lNewSheet.Cells[1, 21];
bottom = lNewSheet.Cells[1, 22];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Merge();
all.Value = "Logical direction";
all.HorizontalAlignment = Microsoft.Office.Interop.Excel.Constants.xlCenter;
lNewSheet.Cells[2, col++] = "Regulon";
lNewSheet.Cells[2, col++] = "Total number in database";
lNewSheet.Cells[2, col++] = "Total number in dataset";
lNewSheet.Cells[2, col++] = string.Format("UP >{0}", Properties.Settings.Default.fcHIGH);
lNewSheet.Cells[2, col++] = string.Format("UP <={0} & >{1}", Properties.Settings.Default.fcHIGH, Properties.Settings.Default.fcMID);
lNewSheet.Cells[2, col++] = string.Format("UP <={0} & >{1}", Properties.Settings.Default.fcMID, Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("UP <={0} & >0", Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("DOWN <0 & >=-{0}", Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("DOWN <-{0} & >=-{1}", Properties.Settings.Default.fcMID, Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("DOWN <=-{0} & >=-{1}", Properties.Settings.Default.fcHIGH, Properties.Settings.Default.fcMID);
lNewSheet.Cells[2, col++] = string.Format("DOWN <-{0}", Properties.Settings.Default.fcHIGH);
lNewSheet.Cells[2, col++] = "Total Relevant";
int colGreen = col;
lNewSheet.Cells[2, col++] = string.Format("UP >{0}", Properties.Settings.Default.fcHIGH);
lNewSheet.Cells[2, col++] = string.Format("UP <={0} & >{1}", Properties.Settings.Default.fcHIGH, Properties.Settings.Default.fcMID);
lNewSheet.Cells[2, col++] = string.Format("UP <={0} & >{1}", Properties.Settings.Default.fcMID, Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("UP <={0} & >0", Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("DOWN <0 & >=-{0}", Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("DOWN <-{0} & >=-{1}", Properties.Settings.Default.fcMID, Properties.Settings.Default.fcLOW);
lNewSheet.Cells[2, col++] = string.Format("DOWN <=-{0} & >=-{1}", Properties.Settings.Default.fcHIGH, Properties.Settings.Default.fcMID);
lNewSheet.Cells[2, col++] = string.Format("DOWN <-{0}", Properties.Settings.Default.fcHIGH);
lNewSheet.Cells[2, col++] = "DOWN";
lNewSheet.Cells[2, col++] = "UP";
// starting from row 3
FastDtToExcel(theTable, lNewSheet, 3, 1, theTable.Rows.Count + 2, theTable.Columns.Count);
// color cells here
top = lNewSheet.Cells[3, colGreen];
bottom = lNewSheet.Cells[theTable.Rows.Count + 2, colGreen+4];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Interior.Color = System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightGreen);
top = lNewSheet.Cells[3, colGreen+4];
bottom = lNewSheet.Cells[theTable.Rows.Count + 2, colGreen + 4+3];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Interior.Color = System.Drawing.ColorTranslator.ToOle(System.Drawing.Color.LightSalmon);
// set number format
top = lNewSheet.Cells[3, 13];
bottom = lNewSheet.Cells[2 + theTable.Rows.Count, 22];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.NumberFormat = "###%";
// fit the width of the columns
top = lNewSheet.Cells[1, 1];
bottom = lNewSheet.Cells[theTable.Rows.Count+2, theTable.Columns.Count];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Columns.AutoFit();
RemoveTask(TASKS.UPDATE_SUMMARY_TABLE);
}
private SysData.DataTable ReformatResults(List<FC_BSU> aList)
{
// find unique regulons
SysData.DataTable lTable = new SysData.DataTable("FC_BSU");
SysData.DataColumn regColumn = new SysData.DataColumn("Regulon", Type.GetType("System.String"));
SysData.DataColumn geneColumn = new SysData.DataColumn("Gene", Type.GetType("System.String"));
SysData.DataColumn pvalColumn = new SysData.DataColumn("Pvalue", Type.GetType("System.Single"));
SysData.DataColumn fcColumn = new SysData.DataColumn("FC", Type.GetType("System.Single"));
SysData.DataColumn dirColumn = new SysData.DataColumn("DIR", Type.GetType("System.Int32"));
lTable.Columns.Add(regColumn);
lTable.Columns.Add(geneColumn);
lTable.Columns.Add(fcColumn);
lTable.Columns.Add(pvalColumn);
lTable.Columns.Add(dirColumn);
for (int r = 0; r < aList.Count; r++)
{
SysData.DataRow lRow = lTable.Rows.Add();
lRow["Regulon"] = aList[r].BSU;
lRow["FC"] = aList[r].FC;
lRow["DIR"] = aList[r].DIR;
lRow["Pvalue"] = aList[r].PVALUE;
lRow["Gene"] = aList[r].GENE;
}
return lTable;
}
private (int,int, int) CalculateFPRatio(SysData.DataRow[] aRow)
{
int nrUP=0, nrDOWN = 0, nrTot=0;
// aRow from an FC_BSU table
for (int i = 0; i < aRow.Length; i++)
{
float fcGene = (float)aRow[i]["FC"];
int dirBSU = (int)aRow[i]["DIR"];
float lowValue = Properties.Settings.Default.fcLOW;
// if upregulated
if (dirBSU < 0)
{
if (fcGene < -lowValue)