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CalcTables.cs
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CalcTables.cs
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using System;
using System.Collections.Generic;
using System.Data;
using System.Linq;
using System.Windows.Forms;
using Excel = Microsoft.Office.Interop.Excel;
using SysData = System.Data;
using static GINtool.ES_Functions;
using Accord.Statistics.Distributions.Univariate;
using static GINtool.ES_Extensions;
using Accord.Math;
using System.Collections;
using System.Windows.Input;
using Accord.Math.Distances;
using System.Windows.Markup;
using Microsoft.Office.Core;
namespace GINtool
{
public partial class GinRibbon
{
/// <summary>
/// Create a summary of regulons and their positive and/or negative associated genes
/// </summary>
/// <param name="theTable"></param>
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, 14];
bottom = lNewSheet.Cells[1, 21];
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, 22];
bottom = lNewSheet.Cells[1, 25];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.Merge();
all.Value = "Probability regulation 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";
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++] = "If activation";
lNewSheet.Cells[2, col++] = "Support";
lNewSheet.Cells[2, col++] = "If repression";
lNewSheet.Cells[2, col++] = "Support";
FastDtToExcel(theTable, lNewSheet, 3, 1, theTable.Rows.Count + 2, theTable.Columns.Count);
// color the blocks of cells... not by direction but just to separate up from down regulated
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 formats for the different types of cells
top = lNewSheet.Cells[3, 13];
bottom = lNewSheet.Cells[2 + theTable.Rows.Count, 22];
all = (Excel.Range)lNewSheet.get_Range(top, bottom);
all.NumberFormat = "###%";
top = lNewSheet.Cells[3, 24];
bottom = lNewSheet.Cells[2 + theTable.Rows.Count, 24];
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);
}
///// <summary>
///// Create a basic count / average usage table per regulon based on the regulon data from subtwiki
///// Because regulator_BSU is not known for all regulators whe use the regulator name
///// </summary>
//private void CreateTableStatistics()
//{
// List<string> lString = new List<string> { Properties.Settings.Default.referenceRegulon };
// SysData.DataTable lUnique = GetDistinctRecords(gRegulonWB, lString.ToArray());
// // initialize the global datatable
// gRefStats = new SysData.DataTable("tblstat");
// int totNrRows = gRegulonWB.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 = gRegulonWB.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 SysData.DataTable MappedCategoryTable()
{
return null;
}
private SysData.DataTable MappedOperonTable()
{
return null;
}
/// <summary>
/// The main routine after mouse selection update. It reads in the data from the excel sheet to return Raw input in a list of BSU structures and a List of genes and their associated regulons
/// </summary>
/// <param name="suppressOutput"></param>
/// <returns></returns>
private List<BsuLinkedItems> ReadDataAndAugment()
{
AddTask(TASKS.READ_SHEET_DATA);
List<Excel.Range> theInputCells = new List<Excel.Range>()
{
gRangeP,
gRangeFC,
gRangeBSU
};
// set flag is data has changed
//if (InputHasChanged() || gOutput == null || gList == null)
if (InputHasChanged() || gList == null || gList.Count==0)
{
gNeedsUpdate = (byte)UPDATE_FLAGS.ALL;
}
else
{
RemoveTask(TASKS.READ_SHEET_DATA);
return gList;
}
int nrRows = gRangeP.Rows.Count;
// generate the results for outputting the data and summary
try
{
//gFgseaHash.Clear();
//gDataSetStat_dict.Clear();
//gGSEADict.Clear();
gBSU_gene_dict.Clear();
List<BsuLinkedItems> lResults = AugmentWithGeneInfo(theInputCells);
if (CanAugmentWithCategoryData())
lResults = AugmentWithCategoryData(lResults);
if (CanAugmentWithRegulonData())
lResults = AugmentWithRegulonData(lResults);
RemoveTask(TASKS.READ_SHEET_DATA);
// make sure that there are no duplicate keys ... not expected
gCombinedDict = gRegulonDict.Concat(gCategoryDict).ToDictionary(kvp => kvp.Key, kvp => kvp.Value);
// CheckValues();
CalibrateES();
return lResults;
}
catch (Exception ex)
{
MessageBox.Show("Are you sure the columns are properly mapped? " + ex.Message);
RemoveTask(TASKS.READ_SHEET_DATA);
return null;
}
}
private void CheckValues()
{
Dictionary<string, int> hashValues = new Dictionary<string, int>();
Dictionary<string, double> signature = getSignature(gDataSetDict, !Properties.Settings.Default.gseaFC);
// gDataSetDict.Where(kvp => kvp.Value.FC != 0).ToDictionary(kvp => kvp.Key, kvp => Math.Sign(kvp.Value.FC) * -Math.Log10(kvp.Value.pval));
//Dictionary<string, double> signature = gDataSetDict.Where(kvp => kvp.Value.FC != 0).ToDictionary(kvp => kvp.Key, kvp => Math.Abs(kvp.Value.FC));
signature = signature.OrderByDescending(x => x.Value).ToDictionary(x => x.Key, x => x.Value);
//dict_rank map_signature = signature.MapRank();
//rank_dict signature_map = signature.RankMap();
//NormalDistribution norm = new NormalDistribution();
string[] signature_genes = signature.Keys.ToArray();
int min_size = 1, max_size = 25000;
foreach (string key in gCombinedDict.Keys)
{
string[] gene_set = gCombinedDict[key];
string[] stripped_set = strip_gene_set(signature_genes, gene_set);
if (stripped_set.Length >= min_size && stripped_set.Length <= max_size)
{
int gsHash = stripped_set.GetHashCodeValue();
hashValues.Add(key, gsHash);
}
string[] gene_set_pos = stripped_set.Where(k => gDataSetDict[k].FC > 0).ToArray();
string[] stripped_set_pos = strip_gene_set(signature_genes, gene_set_pos);
if (stripped_set_pos.Length >= min_size && stripped_set_pos.Length <= max_size)
{
int gsHash = stripped_set_pos.GetHashCodeValue();
hashValues.Add(String.Format("{0}_pos", key), gsHash);
}
string[] gene_set_neg = stripped_set.Where(k => gDataSetDict[k].FC < 0).ToArray();
string[] stripped_set_neg = strip_gene_set(signature_genes, gene_set_neg);
if (stripped_set_neg.Length >= min_size && stripped_set_neg.Length <= max_size)
{
int gsHash = stripped_set_neg.GetHashCodeValue();
hashValues.Add(String.Format("{0}_neg", key), gsHash);
}
}
var distinctList = hashValues.Values.Distinct().ToList();
Dictionary<int, IEnumerable<string>> myDict = new Dictionary<int, IEnumerable<string>>();
foreach(int v in distinctList)
{
IEnumerable<string> myKeys = hashValues.Where(pair => pair.Value == v).Select(pair => pair.Key);
myDict.Add(v, myKeys);
}
//System.IO.File.WriteAllLines(@"c:\temp\pathtocsv.csv", myDict.Select(x => x.Key + "," + String.Join(",",x.Value.ToArray()) + ","));
}
private void CalibrateES()
{
if (gCategoryDict.Count == 0 && gRegulonDict.Count == 0)
return;
AddTask(TASKS.ES_CALIBRATION);
gsea_calibrate(gDataSetDict, gCombinedDict, ref gFgseaHash,pvalues:!Properties.Settings.Default.gseaFC);
RemoveTask(TASKS.ES_CALIBRATION);
AddTask(TASKS.ES_CALCULATION);
gsea_enrich(gDataSetDict, gCombinedDict, gFgseaHash, ref gGSEAHash, min_size: 1, pvalues: !Properties.Settings.Default.gseaFC);
RemoveTask(TASKS.ES_CALCULATION);
CopyStaticESParameters();
}
private void CopyStaticESParameters()
{
gES_signature = getSignature(gDataSetDict,!Properties.Settings.Default.gseaFC);
gES_signature_ordered = gES_signature.OrderByDescending(x => x.Value).ToDictionary(x => x.Key, x => x.Value);
gES_map_signature = gES_signature_ordered.MapRank();
gES_signature_map = gES_signature_ordered.RankMap();
NormalDistribution normal = new NormalDistribution();
gES_signature_genes = gES_signature_ordered.Keys.ToArray();
gES_sigvalues = gES_signature_ordered.Values.ToArray();
gES_sigvalues = gES_sigvalues.Plus(Pmult(normal.Generate(gES_sigvalues.Length), 1 / (gES_sigvalues.Average() * 10000)));
gES_abs_signature = gES_sigvalues.Abs();
Dictionary<string,double> signature_ordered = gES_signature.OrderBy(kvp => kvp.Value).ToDictionary(x => x.Key, x => x.Value);
int sighashK = signature_ordered.Keys.GetHashCodeValue();
int sighashV = signature_ordered.Values.GetHashCodeValue();
int sig_hash = sighashK + sighashV;
gES_key = sighashK + sighashV;
}
private (double,double) CalcES(IEnumerable<string> gene_set)
{
S_GSEA result = gsea_calc(gES_abs_signature, gES_signature_genes, gES_map_signature, gES_signature_map, gene_set, (S_ESPARAMS) gFgseaHash[gES_key], ref gGSEAHash, min_size: 1);
double pval = result.pval == 0 ? 1e-80 : result.pval;
return (result.es, pval);
}
/// <summary>
/// Calculate the nr of genes up-regulated and down-regulated by it's fold change and the expected direction based on the mode of the regulon
/// </summary>
/// <param name="aRow"></param>
/// <returns>repressed up, activated up, repressed down, activated down, total</returns>
private (int, int, int, int, int) CalculateFPRatio(SysData.DataRow[] aRow)
{
int nrActiveUP = 0, nrActiveDOWN = 0, nrRepressUP = 0, nrRepressDown = 0, nrTot = 0;
// aRow from an FC_BSU table
for (int i = 0; i < aRow.Length; i++)
{
double fcGene = (double)aRow[i]["FC"];
int dirBSU = (int)aRow[i]["DIR"];
double lowValue = Properties.Settings.Default.fcLOW;
// if in repressed mode
if (dirBSU < 0)
{
// and fc < -lowValue
if (fcGene < -lowValue)
{
nrRepressUP += 1;
nrTot += 1;
}
// and fc > lowValue
if (fcGene > lowValue)
{
nrRepressDown += 1;
nrTot += 1;
}
}
// if in activated mode
if (dirBSU > 0)
{
// and fc > lowValue
if (fcGene > lowValue)
{
nrActiveUP += 1;
nrTot += 1;
}
// fc < -lowValue
if (fcGene < -lowValue)
{
nrActiveDOWN += 1;
nrTot += 1;
}
}
}
return (nrRepressUP, nrActiveUP, nrRepressDown, nrActiveDOWN, nrTot);
}
/// <summary>
/// Create a combined table that combines the raw data and regulon summaries
/// </summary>
/// <param name="aUsageTbl">the tabel with mapped categories/regulons</param>
/// <param name="lLst"></param>
/// <returns></returns>
private (SysData.DataTable, SysData.DataTable) CreateCombinedTable(SysData.DataTable aUsageTbl, List<BsuLinkedItems> lLst, List<summaryInfo> bestResults)
{
SysData.DataTable lTable = new SysData.DataTable();
SysData.DataTable lColorTable = new SysData.DataTable();
SysData.DataColumn col = new SysData.DataColumn("BSU", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("GENE", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("FC", Type.GetType("System.Double"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("PVALUE", Type.GetType("System.Double"));
lTable.Columns.Add(col);
int maxRegulons = 0;
for (int i = 0; i < lLst.Count; i++)
{
if (maxRegulons < lLst[i].Regulons.Count)
maxRegulons = lLst[i].Regulons.Count;
}
for (int i = 0; i < maxRegulons; i++)
{
col = new SysData.DataColumn(string.Format("Regulon_{0}", i + 1), Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn(string.Format("Regulon_{0}", i + 1), Type.GetType("System.Int16"));
lColorTable.Columns.Add(col);
}
double lowVal = Properties.Settings.Default.fcLOW;
// loop over all the genes found in the data
for (int r = 0; r < lLst.Count; r++)
{
// continue depending on value of lowest fc definition
bool accept = Properties.Settings.Default.use_pvalues ? lLst[r].PVALUE < Properties.Settings.Default.pvalue_cutoff : Math.Abs(lLst[r].FC) > lowVal;
if (accept)
{
SysData.DataRow lColorRow = lColorTable.Rows.Add();
SysData.DataRow lRow = lTable.Rows.Add();
lRow["FC"] = lLst[r].FC;
lRow["BSU"] = lLst[r].BSU;
lRow["GENE"] = lLst[r].GeneName;
lRow["PVALUE"] = lLst[r].PVALUE;
double FC = lLst[r].FC;
for (int i = 0; i < lLst[r].Regulons.Count; i++)
{
// check association direction
bool posAssoc = lLst[r].REGULON_UP.Contains(i);
bool negAssoc = lLst[r].REGULON_DOWN.Contains(i);
// depending on the association in the table the cell color is red or green
int clrInt = posAssoc ? 1 : negAssoc ? -1 : 0;
SysData.DataRow[] lHit = aUsageTbl.Select(string.Format("Regulon = '{0}'", lLst[r].Regulons[i].Name));
double nrUP = Double.Parse(lHit[0]["nr_UP"].ToString());
double nrDOWN = Double.Parse(lHit[0]["nr_DOWN"].ToString());
Double.TryParse(lHit[0]["perc_UP"].ToString(), out double percUP);
Double.TryParse(lHit[0]["perc_DOWN"].ToString(), out double percDOWN);
double percRel = Double.Parse(lHit[0]["totrelperc"].ToString());
string lVal = "";
string _down = "\u2193";
string _up = "\u2191";
// logical association
if ((posAssoc && FC > 0) || (negAssoc && FC < 0))
{
lVal = percUP.ToString("P0") + _up + percRel.ToString("P0") + "-tot";
}
if (nrUP == nrDOWN)
lVal = "0%-" + percRel.ToString("P0") + "-tot";
// false postive/negative
if ((posAssoc && FC < 0) || (negAssoc && FC > 0))
{
lVal = percDOWN.ToString("P0") + _down + percRel.ToString("P0") + "-tot";
}
lRow[string.Format("Regulon_{0}", i + 1)] = lLst[r].Regulons[i] + " " + lVal;
lColorRow[string.Format("Regulon_{0}", i + 1)] = clrInt;
}
}
}
for (int i = maxRegulons; i > 0; i--)
{
string columnName = string.Format("Regulon_{0}", i);
object lRes = lTable.Compute(string.Format("COUNT({0})", columnName), "");
int lCount = Int16.Parse(lRes.ToString());
if (lCount == 0)
{
lTable.Columns.Remove(columnName);
lColorTable.Columns.Remove(columnName);
}
}
return (lTable, lColorTable);
}
/// <summary>
/// Create the data table that can be used to display the data augmented with operon info in an Excel sheet.
/// </summary>
/// <param name="aUsageTbl"></param>
/// <param name="lLst"></param>
/// <returns></returns>
private SysData.DataTable CreateOperonTable(List<BsuLinkedItems> lLst)
{
SysData.DataTable lTable = new SysData.DataTable();
SysData.DataColumn col = new SysData.DataColumn("BSU", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("FC", Type.GetType("System.Double"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("P-value", Type.GetType("System.Double"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("Gene", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("Function", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("Description", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("operon", Type.GetType("System.String"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("nroperons", Type.GetType("System.Int16"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("nrgenes", Type.GetType("System.Int16"));
lTable.Columns.Add(col);
col = new SysData.DataColumn("operon_genes", Type.GetType("System.String"));
lTable.Columns.Add(col);
for (int nr = 0; nr < gMaxGenesPerOperon; nr++) // remove extra columns later if necessary
{
col = new SysData.DataColumn(string.Format("gene_{0}", nr + 1), Type.GetType("System.Double"));
lTable.Columns.Add(col);
}
int maxColumnsUsed = 0;
//List<string> genesIDs = new List<string>();
//foreach(BsuLinkedItems item in lLst)
// genesIDs.Add("'"+item.GeneName+"'");
//string _filter = String.Join(",", genesIDs.ToArray());
//SysData.DataRow[] _lt = gRefOperonsWB.Select(String.Format("gene in ({0})", _filter));
//double lowVal = Properties.Settings.Default.fcLOW;
// loop over the all the genes found
for (int r = 0; r < lLst.Count; r++)
{
string geneName = lLst[r].GeneName;
//double lFC = lLst[r].FC;
//double lPval = lLst[r].PVALUE;
List<string> luOperons = new List<string>();
// possibly multiple operons for a single gene
SysData.DataRow[] lOperons = gRefOperonsWB.Select(string.Format("gene='{0}'", geneName));
string operon = "";
// create a list of 'other' genes
List<string> lgenes = new List<string>();
// create a list of 'other' genes' FCs
List<double> lFCs = new List<double>();
//string opgenes = "";
List<List<string>> llgenes = new List<List<string>>();
int _m = 0;
int _maxm = _m;
// loop over all operons first to determine leading operon .. i.e. the one with the most number of genes associated
foreach (DataRow row in lOperons)
{
luOperons.Add(row["operon"].ToString());
// an operon in return can have multiple genes associated with it.. register it and get the FCs
(List<string> _lgenes, List<double> _lFCs) = GetOperonGenesFC(row["op_id"].ToString(), lLst);
// add to list
llgenes.Add(_lgenes);
// if newly found genes is larger than previously found, store the associated values
if (_lgenes.Count > lgenes.Count)
{
_maxm = _m;
operon = row["operon"].ToString();
lgenes = new List<string>(_lgenes);
lFCs = new List<double>(_lFCs);
}
_m++;
}
// count nr of operons
int noperons = luOperons.Count();
// add a row
SysData.DataRow lRow = lTable.Rows.Add();
lRow["BSU"] = lLst[r].BSU;
lRow["FC"] = lLst[r].FC;
lRow["P-Value"] = lLst[r].PVALUE;
lRow["Function"] = lLst[r].GeneFunction;
lRow["Description"] = lLst[r].GeneDescription;
lRow["gene"] = geneName;
// if any operon is found
if (operon.Length > 0)
{
// assign operon with most genes as leading operon
operon = luOperons[_maxm];
lgenes = llgenes[_maxm];
string opgenes = string.Join("-", lgenes.ToArray());
llgenes.Remove(lgenes);
// combine multiple orperons in a hyphenated string
foreach (List<string> _item in llgenes)
{
opgenes = opgenes + Environment.NewLine + string.Join("-", _item.ToArray());
}
int nrgenes = lgenes.Count;
lRow["operon"] = operon;
lRow["nroperons"] = noperons;
lRow["nrgenes"] = nrgenes;
lRow["operon_genes"] = opgenes;
if (nrgenes > maxColumnsUsed)
maxColumnsUsed = nrgenes;
// copy the FCs
for (int i = 0; i < nrgenes; i++)
{
if (!(lFCs[i] is Double.NaN))
lRow[string.Format("gene_{0}", i + 1)] = lFCs[i];
}
}
}
for (int _g = gMaxGenesPerOperon; _g > maxColumnsUsed; _g--)
{
string colFmt = String.Format("gene_{0}", _g);
lTable.Columns.Remove(colFmt);
}
return lTable;
}
/// <summary>
/// Create the linkage table between regulon and genes
/// </summary>
/// <param name="aList"></param>
/// <returns></returns>
private SysData.DataTable CreateGeneUsageTable(List<BsuLinkedItems> aList)
{
SysData.DataTable lTable = new SysData.DataTable("GeneResultsTable");
SysData.DataColumn geneColumn = new SysData.DataColumn("Gene", Type.GetType("System.String"));
SysData.DataColumn geneIDcolumn = new SysData.DataColumn("Gene_ID", Type.GetType("System.String"));
/* Need to check if we do need all of them */
SysData.DataColumn pvalColumn = new SysData.DataColumn("Pvalue", Type.GetType("System.Double"));
SysData.DataColumn fcColumn = new SysData.DataColumn("FC", Type.GetType("System.Double"));
SysData.DataColumn functionColumn = new SysData.DataColumn("GeneFunction", Type.GetType("System.String"));
SysData.DataColumn decsColumn = new SysData.DataColumn("GeneDescription", Type.GetType("System.String"));
//lTable.Columns.Add(regColumn);
lTable.Columns.Add(geneIDcolumn);
lTable.Columns.Add(geneColumn);
lTable.Columns.Add(fcColumn);
lTable.Columns.Add(pvalColumn);
//lTable.Columns.Add(dirColumn);
lTable.Columns.Add(functionColumn);
lTable.Columns.Add(decsColumn);
foreach (BsuLinkedItems _it in aList)
{
SysData.DataRow lRow = lTable.Rows.Add();
lRow["Gene"] = _it.GeneName;
lRow["Gene_ID"] = _it.BSU;
lRow["FC"] = _it.FC;
lRow["GeneFunction"] = _it.GeneFunction;
lRow["GeneDescription"] = _it.GeneDescription;
lRow["Pvalue"] = _it.PVALUE;
}
return lTable;
}
/// <summary>
/// Create the linkage table between regulon and genes
/// </summary>
/// <param name="aList"></param>
/// <returns></returns>
private SysData.DataTable CreateRegulonUsageTable(List<BsuLinkedItems> aList)
{
SysData.DataTable lTable = new SysData.DataTable("MappedRegulons");
SysData.DataColumn regColumn = new SysData.DataColumn("Regulon", Type.GetType("System.String"));
SysData.DataColumn geneColumn = new SysData.DataColumn("Gene", Type.GetType("System.String"));
SysData.DataColumn geneIDcolumn = new SysData.DataColumn("Gene_ID", Type.GetType("System.String"));
/* Need to check if we do need all of them */
SysData.DataColumn pvalColumn = new SysData.DataColumn("Pvalue", Type.GetType("System.Double"));
SysData.DataColumn fcColumn = new SysData.DataColumn("FC", Type.GetType("System.Double"));
SysData.DataColumn dirColumn = new SysData.DataColumn("DIR", Type.GetType("System.Int32"));
SysData.DataColumn functionColumn = new SysData.DataColumn("GeneFunction", Type.GetType("System.String"));
SysData.DataColumn decsColumn = new SysData.DataColumn("GeneDescription", Type.GetType("System.String"));
lTable.Columns.Add(regColumn);
lTable.Columns.Add(geneIDcolumn);
lTable.Columns.Add(geneColumn);
lTable.Columns.Add(fcColumn);
lTable.Columns.Add(pvalColumn);
lTable.Columns.Add(dirColumn);
lTable.Columns.Add(functionColumn);
lTable.Columns.Add(decsColumn);
foreach (BsuLinkedItems _it in aList)
{
List<RegulonItem> _regulons = _it.Regulons;
foreach (RegulonItem __it in _regulons)
{
SysData.DataRow lRow = lTable.Rows.Add();
lRow["Regulon"] = __it.Name;
lRow["DIR"] = __it.Direction == "UP" ? 1 : ( __it.Direction == "DOWN" ? -1 : 0); // add check for when no direction is given
lRow["Gene_ID"] = _it.BSU;
lRow["Gene"] = _it.GeneName;
lRow["FC"] = _it.FC;
lRow["GeneFunction"] = _it.GeneFunction;
lRow["GeneDescription"] = _it.GeneDescription;
lRow["Pvalue"] = _it.PVALUE;
}
}
return lTable;
}
/// <summary>
/// Create the linkage tables between categories and genes
/// </summary>
/// <param name="aList"></param>
/// <returns></returns>
private SysData.DataTable CreateCategoryUsageTable(List<BsuLinkedItems> aList)
{
SysData.DataTable lTable = new SysData.DataTable("MappedCategories");
SysData.DataColumn regColumn = new SysData.DataColumn("Category", Type.GetType("System.String"));
SysData.DataColumn geneColumn = new SysData.DataColumn("Gene", Type.GetType("System.String"));
SysData.DataColumn geneIDcolumn = new SysData.DataColumn("Gene_ID", Type.GetType("System.String"));
/* Need to check if we do need all of them */
SysData.DataColumn pvalColumn = new SysData.DataColumn("Pvalue", Type.GetType("System.Double"));
SysData.DataColumn fcColumn = new SysData.DataColumn("FC", Type.GetType("System.Double"));
//SysData.DataColumn dirColumn = new SysData.DataColumn("DIR", Type.GetType("System.Int32"));
SysData.DataColumn functionColumn = new SysData.DataColumn("GeneFunction", Type.GetType("System.String"));
SysData.DataColumn decsColumn = new SysData.DataColumn("GeneDescription", Type.GetType("System.String"));
lTable.Columns.Add(regColumn);
lTable.Columns.Add(geneIDcolumn);
lTable.Columns.Add(geneColumn);
lTable.Columns.Add(fcColumn);
lTable.Columns.Add(pvalColumn);
//lTable.Columns.Add(dirColumn);
lTable.Columns.Add(functionColumn);
lTable.Columns.Add(decsColumn);
foreach (BsuLinkedItems _it in aList)
{
List<CategoryItem> _categories = _it.Categories;
foreach (CategoryItem __it in _categories)
{
SysData.DataRow lRow = lTable.Rows.Add();
lRow["Category"] = __it.Name;
lRow["Gene_ID"] = _it.BSU;
lRow["Gene"] = _it.GeneName;
lRow["FC"] = _it.FC;
lRow["GeneFunction"] = _it.GeneFunction;
lRow["GeneDescription"] = _it.GeneDescription;
lRow["Pvalue"] = _it.PVALUE;
}
}
return lTable;
}
/// <summary>
/// Transform the summaryinfo data to the highly specific (i.e. significance ranges) bubbleplot format ready result.
/// </summary>
/// <param name="info"></param>
/// <returns></returns>
private List<element_rank> BubblePlotData(List<summaryInfo> info, bool volcanoPlot=false, int maxExtreme=-1)
{
List<element_rank> element_Ranks = new List<element_rank>();
// MAD values
List<double> e1_m = new List<double>(), e2_m = new List<double>(), e3_m = new List<double>(), e4_m = new List<double>(), e5_m = new List<double>();
// FC values
List<double> e1_fc = new List<double>(), e2_fc = new List<double>(), e3_fc = new List<double>(), e4_fc = new List<double>(), e5_fc = new List<double>();
// Counts
List<int> e1_n = new List<int>(), e2_n = new List<int>(), e3_n = new List<int>(), e4_n = new List<int>(), e5_n = new List<int>();
// p_values
List<double> e1_pv = new List<double>(), e2_pv = new List<double>(), e3_pv = new List<double>(), e4_pv = new List<double>(), e5_pv = new List<double>();
// CATEGORY/REGULON NAMES
List<string> e1_s = new List<string>(), e2_s = new List<string>(), e3_s = new List<string>(), e4_s = new List<string>(), e5_s = new List<string>();
// BEST GENE PERCENTAGES
List<double> e1_p = new List<double>(), e2_p = new List<double>(), e3_p = new List<double>(), e4_p = new List<double>(), e5_p = new List<double>();
double[] pvalues = info.Select(x=>x.p_fdr).OrderBy(x=>x).ToArray();
double[] q = new double[] { 10D, 20D, 33D, 50D };
double[] nn = percentiles(pvalues, q).OrderBy(x=>x).ToArray();
foreach (summaryInfo sInfo in info)
{
double pVal = sInfo.p_fdr;
bool check1 = pVal <= nn[0];
bool check2 = pVal > nn[0] && pVal <= nn[1];
bool check3 = pVal > nn[1] && pVal <= nn[2];
bool check4 = pVal > nn[2] && pVal <= nn[3];
bool check5 = pVal > nn[3];
if (volcanoPlot)
{
check1 = sInfo.best_gene_percentage >= 90;
check2 = sInfo.best_gene_percentage >= 80 && sInfo.best_gene_percentage < 90;
check3 = sInfo.best_gene_percentage >= 75 && sInfo.best_gene_percentage < 80;
check4 = sInfo.best_gene_percentage >= 67 && sInfo.best_gene_percentage < 75;
check5 = sInfo.best_gene_percentage >0 && sInfo.best_gene_percentage < 67;
}
List<double> _workfc = null;
List<double> _workm = null;
List<int> _workn = null;
List<string> _works = null;
List<double> _workp = null;
List<double> _workpv = null;
if (check1 && sInfo.genes[0] != "")
{
_workfc = e1_fc;
_workm = e1_m;
_workn = e1_n;
_works = e1_s;
_workp = e1_p;
_workpv = e1_pv;
}
if (check2 && sInfo.genes[0] != "")
{
_workfc = e2_fc;
_workm = e2_m;
_workn = e2_n;
_works = e2_s;
_workp = e2_p;
_workpv = e2_pv;
}
if (check3 && sInfo.genes[0] != "")
{
_workfc = e3_fc;
_workm = e3_m;
_workn = e3_n;
_works = e3_s;
_workp = e3_p;
_workpv = e3_pv;
}
if (check4 && sInfo.genes[0] != "")
{
_workfc = e4_fc;
_workm = e4_m;
_workn = e4_n;
_works = e4_s;
_workp = e4_p;
_workpv = e4_pv;
}
if (check5 && sInfo.genes[0] != "")
{
_workfc = e5_fc;
_workm = e5_m;
_workn = e5_n;
_works = e5_s;
_workp = e5_p;
_workpv = e5_pv;
}
if (_workfc != null)
{
_workfc.Add(sInfo.fc_average);
_workm.Add(sInfo.fc_mad);
_workn.Add(sInfo.p_values != null ? sInfo.p_values.Length : 0);
double _pVal = -Math.Log10(sInfo.p_fdr);
_workpv.Add( maxExtreme >0 ? (_pVal > maxExtreme ? maxExtreme : _pVal) : _pVal);
_works.Add(StripText(sInfo.catName));
_workp.Add(sInfo.best_gene_percentage);
}
}
string catLabel1 = "<=10%", catLabel2 = "10%-20%", catLabel3 = "20%-33%", catLabel4 = "33%-50%", catLabel5 = ">50%";
if (volcanoPlot)
{
catLabel1 = ">=90";
catLabel2 = ">=80";
catLabel3 = ">=75";
catLabel4 = ">=67";
catLabel5 = ">=50";
}
element_rank e1 = new element_rank()
{
catName = catLabel1,
p_fdr = e1_pv.ToArray(),
average_fc = e1_fc.ToArray(),
mad_fc = e1_m.ToArray(),
nr_genes = e1_n.ToArray(),
genes = e1_s.ToArray(),
best_genes_percentage = e1_p.ToArray()
};
element_rank e2 = new element_rank()
{