//Engine.Evaluate($"png('{ImagePath.Replace('\\', '/') + imagePath + ".png"}', {900}, {600})");
internal static double[] GenerateNormalDistribution(double min, double max, int numberOfFeatures)
{
try
{
/* Engine.Evaluate($"rnorm.between <- function(n, minimum = 0, maximum = 1)");
* Engine.Evaluate("{");
* Engine.Evaluate($"x <- rnorm(n)");
* Engine.Evaluate($"max_x <- max(x)");
* Engine.Evaluate($"min_x <- min(x)");
* Engine.Evaluate($"x <- x - min_x");
* Engine.Evaluate($"x <- x / (max_x - min_x)");
* Engine.Evaluate($"x <- x * (maximum - minimum)");
* Engine.Evaluate($"x <- x + minimum");
* Engine.Evaluate($"return (x)");
* Engine.Evaluate("}");
*/
//var func = Engine.Evaluate("function (n, min, max) {x <- rnorm(n, mean = 0, sd = 1); x <- x - -3; x <- x / (6); x <- x * (min - max); y <- x + min; return (y) }").AsFunction();
var func = Engine.Evaluate(@"function (n, min, max) {
x <- rnorm(n, mean = 0, sd = 1)
x <- x - -3
x <- x / (6)
x <- x * (max - min)
x <- x + min
return (x)
}").AsFunction();
var param1 = Engine.CreateInteger(numberOfFeatures);
var param2 = Engine.CreateNumeric(min);
var param3 = Engine.CreateNumeric(max);
return(func.Invoke(new SymbolicExpression[] { param1, param2, param3 }).AsNumeric().ToArray());
//return Engine.Evaluate($"result <- rnorm.between({numberOfFeatures}, {min}, {max})").AsNumeric().ToArray();
}
catch (Exception e)
{ Console.WriteLine(e.ToString()); return(new double[] { 0 }); }
}
private void SetupDotNetToRConverters()
{
SetupDotNetToRConverter(typeof(void), p => null);
SetupDotNetToRConverter(typeof(string), p => engine.CreateCharacter((string)p));
SetupDotNetToRConverter(typeof(string[]), p => engine.CreateCharacterVector((string[])p));
SetupDotNetToRConverter(typeof(List <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(IList <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(ICollection <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(IEnumerable <string>), p => engine.CreateCharacterVector((IEnumerable <string>)p));
SetupDotNetToRConverter(typeof(string[, ]), p => engine.CreateCharacterMatrix((string[, ])p));
SetupDotNetToRConverter(typeof(int), p => engine.CreateInteger((int)p));
SetupDotNetToRConverter(typeof(int[]), p => engine.CreateIntegerVector((int[])p));
SetupDotNetToRConverter(typeof(List <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(IList <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(ICollection <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(IEnumerable <int>), p => engine.CreateIntegerVector((IEnumerable <int>)p));
SetupDotNetToRConverter(typeof(int[, ]), p => engine.CreateIntegerMatrix((int[, ])p));
SetupDotNetToRConverter(typeof(bool), p => engine.CreateLogical((bool)p));
SetupDotNetToRConverter(typeof(bool[]), p => engine.CreateLogicalVector((bool[])p));
SetupDotNetToRConverter(typeof(List <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(IList <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(ICollection <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(IEnumerable <bool>), p => engine.CreateLogicalVector((IEnumerable <bool>)p));
SetupDotNetToRConverter(typeof(bool[, ]), p => engine.CreateLogicalMatrix((bool[, ])p));
SetupDotNetToRConverter(typeof(double), p => engine.CreateNumeric((double)p));
SetupDotNetToRConverter(typeof(double[]), p => engine.CreateNumericVector((double[])p));
SetupDotNetToRConverter(typeof(List <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(IList <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(ICollection <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(IEnumerable <double>), p => engine.CreateNumericVector((IEnumerable <double>)p));
SetupDotNetToRConverter(typeof(double[, ]), p => engine.CreateNumericMatrix((double[, ])p));
SetupDotNetToRConverter(typeof(DateTime), p => engine.CreatePosixct((DateTime)p));
SetupDotNetToRConverter(typeof(DateTime[]), p => engine.CreatePosixctVector((DateTime[])p));
SetupDotNetToRConverter(typeof(List <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(IList <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(ICollection <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(IEnumerable <DateTime>), p => engine.CreatePosixctVector((IEnumerable <DateTime>)p));
SetupDotNetToRConverter(typeof(DateTime[, ]), p => engine.CreatePosixctMatrix((DateTime[, ])p));
SetupDotNetToRConverter(typeof(TimeSpan), p => engine.CreateDiffTime((TimeSpan)p));
SetupDotNetToRConverter(typeof(TimeSpan[]), p => engine.CreateDiffTimeVector((TimeSpan[])p));
SetupDotNetToRConverter(typeof(List <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(IList <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(ICollection <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(IEnumerable <TimeSpan>), p => engine.CreateDiffTimeVector((IEnumerable <TimeSpan>)p));
SetupDotNetToRConverter(typeof(TimeSpan[, ]), p => engine.CreateDiffTimeMatrix((TimeSpan[, ])p));
}
public override void SetSymbol(REngine rEngine, string name, object value)
{
rEngine.SetSymbol(name, rEngine.CreateInteger((int)value));
}
private void runTask()
{
string basedir = AppDomain.CurrentDomain.BaseDirectory;
string mapPath = basedir + "/tmp/";
// string mapPath = HttpContext.Current.Server.MapPath("~/tmp/");
REngine engine = Utils.getREngineInstance();
string primer3path = System.Web.Configuration.WebConfigurationManager.AppSettings["primer3Home"];
string processNum = System.Web.Configuration.WebConfigurationManager.AppSettings["processNum"];
string isDeleteTempDir = System.Web.Configuration.WebConfigurationManager.AppSettings["deleteTempDir"];
while (true)
{
if (task_queue.Count != 0)
{
Application.Lock();
CustomTask customTask = (CustomTask)task_queue.Dequeue();
Application.UnLock();
customTask.waitQueue = 0;
Object[] task_queue_array = task_queue.ToArray();
for (int i = 0; i < task_queue_array.Length; i++)
{
CustomTask tmpTask = (CustomTask)task_queue_array[i];
tmpTask.waitQueue = i + 1;
}
Application["running_task"] = customTask;
string fileName = customTask.url;
fileName = basedir + "/" + customTask.url;
DataTable dt = read_primer_sequence(fileName);
string[,] primerMat = getPrimerMat(dt);
customTask.status = "preparing ...";
WriteLog(customTask.key, customTask);
CharacterMatrix primer = engine.CreateCharacterMatrix(primerMat);
string rand_file = System.IO.Path.GetRandomFileName();
string tmp_path = mapPath + rand_file;
//string primer3path = "D:/Install/primer3-win-bin-2.3.6";
if (Directory.Exists(tmp_path))
{
DirectoryInfo di = new DirectoryInfo(tmp_path);
di.Delete(true);
}
else if (File.Exists(tmp_path))
{
FileInfo fi = new FileInfo(tmp_path);
fi.Delete();
}
Directory.CreateDirectory(tmp_path);
engine.Evaluate("library(xlsx)");
customTask.percent = 8;
string script_path = basedir + "/primer_dimer_check.R";
script_path = script_path.Replace(@"\", @"/");
engine.Evaluate("source(\"" + script_path + "\")");
customTask.percent = 10;
engine.SetSymbol("primer", primer);
engine.SetSymbol("tmp_dir", engine.CreateCharacter(tmp_path));
engine.SetSymbol("primer", primer);
engine.SetSymbol("primer3dir", engine.CreateCharacter(primer3path));
int?nProcess = Convert.ToInt32(processNum);
if (nProcess != null)
{
engine.SetSymbol("nprocess", engine.CreateInteger(Convert.ToInt32(nProcess)));
}
else
{
engine.SetSymbol("nprocess", engine.CreateInteger(4));
}
engine.SetSymbol("outputfile", engine.CreateCharacter(fileName));
string[] bat_cmds = engine.Evaluate("prepare_bat(tmp_dir,primer,primer3dir,nprocess)").AsCharacter().ToArray();
customTask.status = "dimer calculating ...";
customTask.percent = 20;
WriteLog(customTask.key, customTask);
AutoResetEvent[] resets = new AutoResetEvent[bat_cmds.Length];
for (int i = 0; i < bat_cmds.Length; i++)
{
resets[i] = new AutoResetEvent(false);
Global.ThreadTransfer transfer = new Global.ThreadTransfer(bat_cmds[i], resets[i]);
Thread thread = new Thread(new ParameterizedThreadStart(run_cmd));
thread.Start(transfer);
}
foreach (var v in resets)
{
v.WaitOne();
customTask.percent += 60 / resets.Length;
}
customTask.status = "result generating ...";
customTask.percent = 80;
WriteLog(customTask.key, customTask);
engine.Evaluate("output_result(tmp_dir,primer,outputfile)");
if (isDeleteTempDir == "true")
{
DirectoryInfo di = new DirectoryInfo(tmp_path);
di.Delete(true);
}
customTask.status = "complete";
customTask.percent = 100;
WriteLog(customTask.key, customTask);
Application["running_task"] = null;
}
}
}
private void button4_Click(object sender, EventArgs e)
{
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
List <double> prob = new List <double>();
List <double> stat = new List <double>();
List <double> pvalue = new List <double>();
double[] bonferroni = new double[FeatureNum];
double[] fdr = new double[FeatureNum];
//int length;
int NAnum = 0;
REngine.SetEnvironmentVariables();
REngine MSS = REngine.GetInstance();
MSS.Initialize();
NumericMatrix Freq = MSS.CreateNumericMatrix(app.FreqMatrix);
MSS.SetSymbol("Freq", Freq);
NumericMatrix Count = MSS.CreateNumericMatrix(app.CountMatrix);
MSS.SetSymbol("Count", Count);
CharacterVector SampleName = MSS.CreateCharacterVector(app.SamName);
CharacterVector FeatureName = MSS.CreateCharacterVector(app.FeaName);
MSS.SetSymbol("FeatureName", FeatureName);
MSS.SetSymbol("SampleName", SampleName);
List <string> SampleNameFreq = new List <string>();
for (int i = 0; i < SampleNum; i++)
{
SampleNameFreq.Add(SampleName[i] + "Freq");
}
IntegerVector RFeaNum = MSS.CreateInteger(FeatureNum);
NumericVector Ralpha = MSS.CreateNumeric(double.Parse(this.textBox1.Text.ToString()));
MSS.SetSymbol("n", RFeaNum);
MSS.SetSymbol("alpha", Ralpha);
List <List <double> > Freqtemp = new List <List <double> >();
List <double> FreqSum = new List <double>();
MSS.Evaluate("leastnum = ceiling ( qnorm(alpha/2)^2 )");
double leastnum = MSS.Evaluate("leastnum").AsNumeric().First();
if (this.comboBox1.SelectedIndex == 0)
{
for (int i = 0; i < FeatureNum; i++)
{
pvalue.Add(100);
for (int j = 0; j < SampleNum - 1; j++)
{
for (int k = j + 1; k < SampleNum; k++)
{
double probtemp = (app.CountMatrix[i, j] + app.CountMatrix[i, k]) / (app.SampleTotal[j] + app.SampleTotal[k]);
double stattemp = (app.FreqMatrix[i, j] - app.FreqMatrix[i, k]) / Math.Sqrt(probtemp * (1 - probtemp) * (1 / app.SampleTotal[j] + 1 / app.SampleTotal[k]));
if (double.IsNaN(stattemp))
{
stattemp = 0;
}
NumericVector Rstat = MSS.CreateNumeric(stattemp);
MSS.SetSymbol("stat", Rstat);
MSS.Evaluate("p.value <- 2*(pnorm(-abs(stat)))");
double pvaluetemp;
if ((this.comboBox2.SelectedIndex == 1) && (app.CountMatrix[i, j] < leastnum) && (app.CountMatrix[i, k] < leastnum))
{
pvaluetemp = 100;
}
else
{
pvaluetemp = MSS.GetSymbol("p.value").AsNumeric().First();
}
if (pvaluetemp != 100)
{
pvalue[i] = Math.Min((double)pvalue[i], (double)pvaluetemp);
}
}
}
}
NumericVector Rpvalue = MSS.CreateNumericVector(pvalue);
MSS.SetSymbol("p.value", Rpvalue);
MSS.Evaluate("NAnum = length(p.value[p.value == 100])");
NAnum = Convert.ToInt32(MSS.GetSymbol("NAnum").AsNumeric().First());
MSS.Evaluate("p.value[p.value == 100] = NA");
MSS.Evaluate("bonferroni.p <- p.adjust(p.value,\"bonferroni\")");
MSS.Evaluate("bonferroni.p[which(bonferroni.p == NA)] = 100");
MSS.Evaluate("fdr.p <- p.adjust(p.value,\"fdr\")");
MSS.Evaluate("fdr.p[which(fdr.p == NA)] = 100");
for (int i = 0; i < FeatureNum; i++)
{
bonferroni[i] = MSS.GetSymbol("bonferroni.p").AsNumeric()[i];
fdr[i] = MSS.GetSymbol("fdr.p").AsNumeric()[i];
}
}
else if (this.comboBox1.SelectedIndex == 1)
{
for (int i = 0; i < FeatureNum; i++)
{
pvalue.Add(100);
}
for (int j = 0; j < SampleNum - 1; j++)
{
for (int k = 1; k < SampleNum; k++)
{
double Sum1 = 0;
double Sum2 = 0;
for (int i = 0; i < FeatureNum; i++)
{
Sum1 = Sum1 + app.CountMatrix[i, j];
Sum2 = Sum2 + app.CountMatrix[i, k];
}
for (int i = 0; i < FeatureNum; i++)
{
NumericVector n11 = MSS.CreateNumeric(app.CountMatrix[i, j]);
NumericVector n21 = MSS.CreateNumeric(app.CountMatrix[i, k]);
NumericVector n12 = MSS.CreateNumeric(Sum1 - app.CountMatrix[i, j]);
NumericVector n22 = MSS.CreateNumeric(Sum2 - app.CountMatrix[i, k]);
MSS.SetSymbol("n11", n11);
MSS.SetSymbol("n12", n12);
MSS.SetSymbol("n21", n21);
MSS.SetSymbol("n22", n22);
MSS.Evaluate("compare <- matrix(c(n11,n12,n21,n22),nr=2)");
MSS.Evaluate("p.value <- fisher.test(compare)$p.value");
double pvaluetemp = MSS.GetSymbol("p.value").AsNumeric().First();
pvalue[i] = Math.Min((double)pvalue[i], (double)pvaluetemp);
}
}
}
MSS.Evaluate("bonferroni.p <- p.adjust(p.value,\"bonferroni\")");
MSS.Evaluate("fdr.p <- p.adjust(p.value,\"fdr\")");
for (int i = 0; i < FeatureNum; i++)
{
bonferroni[i] = MSS.GetSymbol("bonferroni.p").AsNumeric()[i];
fdr[i] = MSS.GetSymbol("fdr.p").AsNumeric()[i];
}
}
List <string> Annotation = new List <string>();
if (this.checkBox1.Checked)
{
if (this.radioButton2.Checked)
{
string strConnCOG;
strConnCOG = "Provider=Microsoft.ACE.OLEDB.12.0;" + "Data Source=" + System.Windows.Forms.Application.StartupPath + "/COG.xlsx" + ";" + "Extended Properties=\"Excel 12.0;HDR=YES;IMEX=1\"";
OleDbConnection OleConnCOG = new OleDbConnection(strConnCOG);
OleConnCOG.Open();
String sqlCOG = "SELECT * FROM [Sheet1$]";
OleDbDataAdapter OleDaExcelCOG = new OleDbDataAdapter(sqlCOG, OleConnCOG);
app.OleDsExcleCOG = new DataSet();
OleDaExcelCOG.Fill(app.OleDsExcleCOG, "Sheet1");
OleConnCOG.Close();
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < app.OleDsExcleCOG.Tables[0].Rows.Count; j++)
{
if (string.Equals(FeatureName[i], app.OleDsExcleCOG.Tables[0].Rows[j][0].ToString()))
{
Annotation.Add(app.OleDsExcleCOG.Tables[0].Rows[j][1].ToString());
}
}
if (Annotation.Count < i + 1)
{
Annotation.Add("No Annotation!");
}
}
}
else if (this.radioButton1.Checked)
{
string strConnPFAM;
strConnPFAM = "Provider=Microsoft.ACE.OLEDB.12.0;" + "Data Source=" + System.Windows.Forms.Application.StartupPath + "/PFAM.xlsx" + ";" + "Extended Properties=\"Excel 12.0;HDR=YES;IMEX=1\"";
OleDbConnection OleConnPFAM = new OleDbConnection(strConnPFAM);
OleConnPFAM.Open();
String sqlPFAM = "SELECT * FROM [Sheet1$]";
OleDbDataAdapter OleDaExcelPFAM = new OleDbDataAdapter(sqlPFAM, OleConnPFAM);
app.OleDsExclePFAM = new DataSet();
OleDaExcelPFAM.Fill(app.OleDsExclePFAM, "Sheet1");
OleConnPFAM.Close();
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < app.OleDsExclePFAM.Tables[0].Rows.Count; j++)
{
if (string.Equals(FeatureName[i], app.OleDsExclePFAM.Tables[0].Rows[j][0].ToString()))
{
Annotation.Add(app.OleDsExclePFAM.Tables[0].Rows[j][1].ToString());
}
}
if (Annotation.Count < i + 1)
{
Annotation.Add("No Annotation!");
}
}
}
}
DataTable dt = new DataTable();
dt.Columns.Add("Feature", typeof(string));
for (int i = 0; i < SampleNum; i++)
{
dt.Columns.Add(app.SamName[i], typeof(double));
}
dt.Columns.Add("p.value", typeof(double));
dt.Columns.Add("bonferroni.p", typeof(double));
dt.Columns.Add("fdr.p", typeof(double));
dt.Columns.Add("Annotation", typeof(string));
for (int i = 0; i < SampleNum; i++)
{
dt.Columns.Add(SampleNameFreq[i], typeof(double));
}
for (int i = 0; i < FeatureNum; i++)
{
DataRow dr = dt.NewRow();
dr[0] = FeatureName[i];
for (int j = 1; j < SampleNum + 1; j++)
{
dr[j] = app.CountMatrix[i, j - 1];
}
if (pvalue[i] == 100)
{
dr[SampleNum + 1] = DBNull.Value;
dr[SampleNum + 2] = DBNull.Value;
dr[SampleNum + 3] = DBNull.Value;
}
else
{
dr[SampleNum + 1] = pvalue[i];
dr[SampleNum + 2] = bonferroni[i];
dr[SampleNum + 3] = fdr[i];
}
if (this.checkBox1.Checked)
{
dr[SampleNum + 4] = Annotation[i];
}
else
{
dr[SampleNum + 4] = null;
}
for (int j = 0; j < SampleNum; j++)
{
dr[j + SampleNum + 5] = app.FreqMatrix[i, j];
}
dt.Rows.Add(dr);
}
DataTable dtCopy = dt.Copy();
DataTable dttemp = dt.Copy();
dttemp.Clear();
DataView dv = dt.DefaultView;
dv.Sort = "p.value";
dtCopy = dv.ToTable();
for (int i = 0; i < NAnum; i++)
{
DataRow row = dtCopy.Rows[i];
dttemp.Rows.Add(row.ItemArray);
}
for (int i = 0; i < NAnum; i++)
{
dtCopy.Rows.RemoveAt(0);
}
dtCopy.Merge(dttemp);
Microsoft.Office.Interop.Excel.Application xlApp = new Microsoft.Office.Interop.Excel.Application();
System.Globalization.CultureInfo CurrentCI = System.Threading.Thread.CurrentThread.CurrentCulture;
System.Threading.Thread.CurrentThread.CurrentCulture = new System.Globalization.CultureInfo("en-US");
Microsoft.Office.Interop.Excel.Workbooks workbooks = xlApp.Workbooks;
Microsoft.Office.Interop.Excel.Workbook workbook = workbooks.Add(Microsoft.Office.Interop.Excel.XlWBATemplate.xlWBATWorksheet);
Microsoft.Office.Interop.Excel.Worksheet worksheet = (Microsoft.Office.Interop.Excel.Worksheet)workbook.Worksheets[1];
Microsoft.Office.Interop.Excel.Range range;
long totalCount = dtCopy.Rows.Count;
long rowRead = 0;
float percent = 0;
for (int i = 0; i < dtCopy.Columns.Count - SampleNum; i++)
{
worksheet.Cells[1, i + 1] = dtCopy.Columns[i].ColumnName;
range = (Microsoft.Office.Interop.Excel.Range)worksheet.Cells[1, i + 1];
range.Interior.ColorIndex = 15;
range.Font.Bold = true;
}
for (int r = 0; r < dtCopy.Rows.Count; r++)
{
for (int i = 0; i < dtCopy.Columns.Count - SampleNum; i++)
{
worksheet.Cells[r + 2, i + 1] = dtCopy.Rows[r][i].ToString();
}
rowRead++;
percent = ((float)(100 * rowRead)) / totalCount;
}
xlApp.Visible = true;
int pnum = 0;
for (int i = 0; i < FeatureNum; i++)
{
try
{
if (double.Parse(dtCopy.Rows[i][SampleNum].ToString()) < double.Parse(this.textBox1.Text.ToString()))
{
pnum++;
}
}
catch
{ }
}
double[,] df = new double[Math.Min(10, FeatureNum), SampleNum];
for (int i = 0; i < Math.Min(10, FeatureNum); i++)
{
for (int j = 0; j < SampleNum; j++)
{
df[i, j] = double.Parse(dtCopy.Rows[i][SampleNum + 5 + j].ToString());
}
}
if (this.checkBox2.Checked)
{
string[] rownamesdf = new string[Math.Min(10, FeatureNum)];
for (int i = 0; i < Math.Min(10, FeatureNum); i++)
{
rownamesdf[i] = dtCopy.Rows[i][0].ToString();
}
CharacterVector Rrownamesdf = MSS.CreateCharacterVector(rownamesdf);
MSS.SetSymbol("Rownamedf", Rrownamesdf);
NumericMatrix Rdf = MSS.CreateNumericMatrix(df);
MSS.SetSymbol("Freqdf", Rdf);
NumericVector RRow = MSS.CreateNumeric(Math.Min(10, FeatureNum));
MSS.SetSymbol("selrow", RRow);
MSS.Evaluate("Freqdf <- as.data.frame(Freqdf)");
MSS.Evaluate("rownames(Freqdf) <- Rownamedf");
MSS.Evaluate("colnames(Freqdf) <- SampleName");
MSS.Evaluate("colournum <- rainbow(dim(Freqdf)[2])");
MSS.Evaluate("plotdata <- t(Freqdf)");
MSS.Evaluate("windows()");
MSS.Evaluate("barplot(plotdata,main=\"features with top varition\",ylab=\"Freq\",beside=TRUE,horiz=FALSE, cex.names=0.6,col=colournum)");
MSS.Evaluate("legend(\"topright\",SampleName,fill=colournum)");
}
if (pnum > 0)
{
double[,] dfall = new double[pnum, SampleNum];
for (int i = 0; i < pnum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
dfall[i, j] = double.Parse(dtCopy.Rows[i][SampleNum + 5 + j].ToString());
}
}
string[] rownamesall = new string[pnum];
for (int i = 0; i < pnum; i++)
{
rownamesall[i] = dtCopy.Rows[i][0].ToString();
}
CharacterVector Rrownamesall = MSS.CreateCharacterVector(rownamesall);
MSS.SetSymbol("Rownameall", Rrownamesall);
NumericMatrix Rdfall = MSS.CreateNumericMatrix(dfall);
MSS.SetSymbol("Freqdfall", Rdfall);
NumericVector RRowall = MSS.CreateNumeric(pnum);
MSS.SetSymbol("selrowall", RRowall);
MSS.Evaluate("Freqdfall <- as.data.frame(Freqdfall)");
MSS.Evaluate("rownames(Freqdfall) <- Rownameall");
MSS.Evaluate("colnames(Freqdfall) <- SampleName");
MSS.Evaluate("distance <- as.dist(1-abs(cor(Freqdfall)))");
if (this.checkBox3.Checked)
{
MSS.Evaluate("fit <- cmdscale(distance, eig=TRUE, k=2)");
MSS.Evaluate("x <- fit$points[,1]");
MSS.Evaluate("y <- fit$points[,2]");
MSS.Evaluate("minx <- min(x)");
MSS.Evaluate("miny <- min(y)");
MSS.Evaluate("maxx <- max(x)");
MSS.Evaluate("maxy <- max(y)");
MSS.Evaluate("randx <- maxx - minx");
MSS.Evaluate("randy <- maxy - miny");
MSS.Evaluate("llimx <- minx - randx/10");
MSS.Evaluate("hlimx <- maxx + randx/3");
MSS.Evaluate("llimy <- miny - randy/10");
MSS.Evaluate("hlimy <- maxy + randy/3");
MSS.Evaluate("windows()");
MSS.Evaluate("plot(x,y,xlab=\"Coordinate 1\",ylab=\"Coordinate 2\",main=\"MDS\", pch=c(0,1,2,5,6), col=rainbow(7), type=\"p\",xlim = c(llimx,hlimx), ylim = c(llimy,hlimy))");
if (this.comboBox3.SelectedIndex == 0)
{
MSS.Evaluate("legend(\"topright\",colnames(Freqdfall),pch=c(0,1,2,5,6),col=rainbow(7),cex = 0.8)");
}
else if (this.comboBox3.SelectedIndex == 1)
{
MSS.Evaluate("text(x,y,labels=SampleName,pos=4)");
}
}
if (this.checkBox4.Checked)
{
MSS.Evaluate("windows()");
MSS.Evaluate("plot(hclust(distance),main =\"Samples Clust\")");
}
}
else
{
MessageBox.Show("No differntially abundant features!!");
}
if (this.checkBox5.Checked)
{
int Rownum = 0;
for (int i = 0; i < FeatureNum; i++)
{
double tempSum = 0;
double tempMean = 0;
for (int j = 0; j < SampleNum; j++)
{
tempSum = tempSum + app.FreqMatrix[i, j];
}
tempMean = tempSum / (SampleNum);
if (tempSum > 0)
{
FreqSum.Add(tempSum);
List <double> tempRow = new List <double>();
for (int j = 0; j < SampleNum; j++)
{
tempRow.Add(app.FreqMatrix[i, j] / tempMean);
}
Freqtemp.Add(tempRow);
Rownum = Rownum + 1;
}
}
for (int i = 0; i < Rownum; i++)
{
for (int j = 0; j < SampleNum; j++)
{
Freqtemp[i][j] = Math.Log(Freqtemp[i][j], 2);
if (Freqtemp[i][j] > 1)
{
Freqtemp[i][j] = 1;
}
else if (Freqtemp[i][j] < -1)
{
Freqtemp[i][j] = -1;
}
}
}
double[,] dfhm = new double[Math.Min(500, Rownum), SampleNum];
for (int i = 0; i < Math.Min(500, Rownum); i++)
{
for (int j = 0; j < SampleNum; j++)
{
dfhm[i, j] = double.Parse(Freqtemp[i][j].ToString());
}
}
string[] rownameshm = new string[Math.Min(500, Rownum)];
for (int i = 0; i < Math.Min(500, Rownum); i++)
{
rownameshm[i] = dtCopy.Rows[i][0].ToString();
}
CharacterVector Rrownameshm = MSS.CreateCharacterVector(rownameshm);
MSS.SetSymbol("Rownamehm", Rrownameshm);
NumericMatrix Rdfhm = MSS.CreateNumericMatrix(dfhm);
MSS.SetSymbol("Freqdfhm", Rdfhm);
NumericVector RRowhm = MSS.CreateNumeric(Math.Min(500, Rownum));
MSS.SetSymbol("plotnum", RRowhm);
MSS.Evaluate("Freqdfhm <- as.data.frame(Freqdfhm)");
MSS.Evaluate("rownames(Freqdfhm) <- Rownamehm");
MSS.Evaluate("colnames(Freqdfhm) <- SampleName");
MSS.Evaluate("Freqdfhm <- as.matrix(Freqdfhm)");
MSS.Evaluate("library(pheatmap)");
MSS.Evaluate("windows()");
if (this.checkBox6.Checked)
{
if (this.checkBox7.Checked)
{
MSS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=T,cluster_rows=T)");
}
else
{
MSS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=F,cluster_rows=T)");
}
}
else
{
if (this.checkBox7.Checked)
{
MSS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=T,cluster_rows=F)");
}
else
{
MSS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=F,cluster_rows=F)");
}
}
}
this.Close();
}
public DataTable getCorpTable(string Rname, int stocknum)
{
engine.Initialize();
string fullRFilePath = Path.Combine(currentPath, Rname + ".R");
if (!File.Exists(fullRFilePath))
{
return(null);
}
var curPath = engine.CreateCharacter(currentPath);
engine.SetSymbol("stocknum", engine.CreateInteger(stocknum));
engine.SetSymbol("curPath", curPath);
engine.Evaluate("setwd(curPath)");
engine.Evaluate(String.Format("source(\"{0}\")", Rname + ".R"));
DataFrame output = engine.GetSymbol("output").AsDataFrame();
DataTable table = new DataTable();
table.Columns.Add("Included", typeof(bool));
foreach (var name in output.ColumnNames)
{
Type t;
switch (output[name].Type)
{
case SymbolicExpressionType.NumericVector:
t = typeof(double); break;
case SymbolicExpressionType.IntegerVector:
t = typeof(Int32); break;
case SymbolicExpressionType.CharacterVector:
t = typeof(string); break;
case SymbolicExpressionType.LogicalVector:
t = typeof(bool); break;
case SymbolicExpressionType.RawVector:
t = typeof(byte); break;
default: t = null; break;
}
table.Columns.Add(name);
if (t != null)
{
table.Columns[name].DataType = t;
}
}
foreach (DataFrameRow row in output.GetRows())
{
DataRow newRow = table.Rows.Add();
newRow["Included"] = true;
foreach (var name in output.ColumnNames)
{
if ((output[name].Type == SymbolicExpressionType.NumericVector ||
output[name].Type == SymbolicExpressionType.IntegerVector) &&
!(name.Contains("현재가") || name.Contains("배당") || name.Contains("RANK")))
{
newRow[name] = (double.Parse(row[name].ToString())) / 1e8;
}
else
{
newRow[name] = row[name];
}
}
}
return(table);
}
private void button4_Click(object sender, EventArgs e)
{
int FeatureNum = app.FeaName.GetLength(0);
int SampleNum = app.SamName.GetLength(0);
List <double> prob = new List <double>();
List <double> stat = new List <double>();
List <double> pvalue = new List <double>();
double[] bonferroni = new double[FeatureNum];
double[] fdr = new double[FeatureNum];
int NAnum = 0;
if (SampleNum == 2)
{
REngine.SetEnvironmentVariables();
REngine TSS = REngine.GetInstance();
TSS.Initialize();
NumericMatrix Freq = TSS.CreateNumericMatrix(app.FreqMatrix);
TSS.SetSymbol("Freq", Freq);
NumericMatrix Count = TSS.CreateNumericMatrix(app.CountMatrix);
TSS.SetSymbol("Count", Count);
CharacterVector SampleName = TSS.CreateCharacterVector(app.SamName);
CharacterVector FeatureName = TSS.CreateCharacterVector(app.FeaName);
TSS.SetSymbol("FeatureName", FeatureName);
TSS.SetSymbol("SampleName", SampleName);
List <string> SampleNameFreq = new List <string>();
for (int i = 0; i < SampleNum; i++)
{
SampleNameFreq.Add(SampleName[i] + "Freq");
}
IntegerVector RFeaNum = TSS.CreateInteger(FeatureNum);
NumericVector Ralpha = TSS.CreateNumeric(double.Parse(this.textBox1.Text.ToString()));
TSS.SetSymbol("n", RFeaNum);
TSS.SetSymbol("alpha", Ralpha);
TSS.Evaluate("leastnum = ceiling ( qnorm(alpha/2)^2 )");
double leastnum = TSS.Evaluate("leastnum").AsNumeric().First();
if (this.comboBox1.SelectedIndex == 0)
{
for (int i = 0; i < FeatureNum; i++)
{
double temp = app.FreqMatrix[i, 0] - app.FreqMatrix[i, 1];
prob.Add(temp);
double P = (app.CountMatrix[i, 0] + app.CountMatrix[i, 1]) / (app.SampleTotal[0] + app.SampleTotal[1]);
double S = Math.Sqrt(P * (1 - P) * (1 / app.SampleTotal[0] + 1 / app.SampleTotal[1]));
double temp0 = prob[i] / S;
if (double.IsNaN(temp0))
{
temp0 = 0;
}
stat.Add(temp0);
}
for (int i = 0; i < FeatureNum; i++)
{
NumericVector Rstat = TSS.CreateNumeric(stat[i]);
TSS.SetSymbol("stat", Rstat);
TSS.Evaluate("p.value <- 2*(pnorm(-abs(stat)))");
if ((this.comboBox2.SelectedIndex == 1) && (app.CountMatrix[i, 0] < leastnum) && (app.CountMatrix[i, 1] < leastnum))
{
pvalue.Add(100);
}
else
{
pvalue.Add(TSS.GetSymbol("p.value").AsNumeric().First());
}
}
NumericVector Rpvalue = TSS.CreateNumericVector(pvalue);
TSS.SetSymbol("p.value", Rpvalue);
TSS.Evaluate("NAnum = length(p.value[p.value == 100])");
NAnum = Convert.ToInt32(TSS.GetSymbol("NAnum").AsNumeric().First());
TSS.Evaluate("p.value[p.value == 100] = NA");
TSS.Evaluate("bonferroni.p <- p.adjust(p.value,\"bonferroni\")");
TSS.Evaluate("bonferroni.p[which(bonferroni.p == NA)] = 100");
//double[] temp1 = (double[])hc1.GetSymbol("bonferroni.p");
TSS.Evaluate("fdr.p <- p.adjust(p.value,\"fdr\")");
TSS.Evaluate("fdr.p[which(fdr.p == NA)] = 100");
for (int i = 0; i < FeatureNum; i++)
{
bonferroni[i] = TSS.GetSymbol("bonferroni.p").AsNumeric()[i];
fdr[i] = TSS.GetSymbol("fdr.p").AsNumeric()[i];
}
}
else if (this.comboBox1.SelectedIndex == 1)
{
double Sum1 = 0;
double Sum2 = 0;
for (int i = 0; i < FeatureNum; i++)
{
Sum1 = Sum1 + app.CountMatrix[i, 0];
Sum2 = Sum2 + app.CountMatrix[i, 1];
}
for (int i = 0; i < FeatureNum; i++)
{
NumericVector n11 = TSS.CreateNumeric(app.CountMatrix[i, 0]);
NumericVector n21 = TSS.CreateNumeric(app.CountMatrix[i, 1]);
NumericVector n12 = TSS.CreateNumeric(Sum1 - app.CountMatrix[i, 0]);
NumericVector n22 = TSS.CreateNumeric(Sum2 - app.CountMatrix[i, 1]);
TSS.SetSymbol("n11", n11);
TSS.SetSymbol("n12", n12);
TSS.SetSymbol("n21", n21);
TSS.SetSymbol("n22", n22);
TSS.Evaluate("compare <- matrix(c(n11,n12,n21,n22),nr=2)");
TSS.Evaluate("p.value <- fisher.test(compare)$p.value");
pvalue.Add(TSS.GetSymbol("p.value").AsNumeric().First());
}
NumericVector Rpvalue = TSS.CreateNumericVector(pvalue);
TSS.SetSymbol("p.value", Rpvalue);
TSS.Evaluate("bonferroni.p <- p.adjust(p.value,\"bonferroni\")");
TSS.Evaluate("fdr.p <- p.adjust(p.value,\"fdr\")");
for (int i = 0; i < FeatureNum; i++)
{
bonferroni[i] = TSS.GetSymbol("bonferroni.p").AsNumeric()[i];
fdr[i] = TSS.GetSymbol("fdr.p").AsNumeric()[i];
}
}
List <string> Annotation = new List <string>();
if (this.checkBox1.Checked)
{
if (this.radioButton1.Checked)
{
string strConnCOG;
strConnCOG = "Provider=Microsoft.ACE.OLEDB.12.0;" + "Data Source=" + System.Windows.Forms.Application.StartupPath + "/COG.xlsx" + ";" + "Extended Properties=\"Excel 12.0;HDR=YES;IMEX=1\"";
OleDbConnection OleConnCOG = new OleDbConnection(strConnCOG);
OleConnCOG.Open();
String sqlCOG = "SELECT * FROM [Sheet1$]";
OleDbDataAdapter OleDaExcelCOG = new OleDbDataAdapter(sqlCOG, OleConnCOG);
app.OleDsExcleCOG = new DataSet();
OleDaExcelCOG.Fill(app.OleDsExcleCOG, "Sheet1");
OleConnCOG.Close();
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < app.OleDsExcleCOG.Tables[0].Rows.Count; j++)
{
if (string.Equals(FeatureName[i], app.OleDsExcleCOG.Tables[0].Rows[j][0].ToString()))
{
Annotation.Add(app.OleDsExcleCOG.Tables[0].Rows[j][1].ToString());
}
}
if (Annotation.Count < i + 1)
{
Annotation.Add("No Annotation!");
}
}
}
else if (this.radioButton2.Checked)
{
string strConnPFAM;
strConnPFAM = "Provider=Microsoft.ACE.OLEDB.12.0;" + "Data Source=" + System.Windows.Forms.Application.StartupPath + "/PFAM.xlsx" + ";" + "Extended Properties=\"Excel 12.0;HDR=YES;IMEX=1\"";
OleDbConnection OleConnPFAM = new OleDbConnection(strConnPFAM);
OleConnPFAM.Open();
String sqlPFAM = "SELECT * FROM [Sheet1$]";
OleDbDataAdapter OleDaExcelPFAM = new OleDbDataAdapter(sqlPFAM, OleConnPFAM);
app.OleDsExclePFAM = new DataSet();
OleDaExcelPFAM.Fill(app.OleDsExclePFAM, "Sheet1");
OleConnPFAM.Close();
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < app.OleDsExclePFAM.Tables[0].Rows.Count; j++)
{
if (string.Equals(FeatureName[i], app.OleDsExclePFAM.Tables[0].Rows[j][0].ToString()))
{
Annotation.Add(app.OleDsExclePFAM.Tables[0].Rows[j][1].ToString());
}
}
if (Annotation.Count < i + 1)
{
Annotation.Add("No Annotation!");
}
}
}
}
DataTable dt = new DataTable();
dt.Columns.Add("Feature", typeof(string));
for (int i = 0; i < SampleNum; i++)
{
dt.Columns.Add(app.SamName[i], typeof(double));
}
dt.Columns.Add("p.value", typeof(double));
dt.Columns.Add("bonferroni.p", typeof(double));
dt.Columns.Add("fdr.p", typeof(double));
dt.Columns.Add("Annotation", typeof(string));
for (int i = 0; i < SampleNum; i++)
{
dt.Columns.Add(SampleNameFreq[i], typeof(double));
}
for (int i = 0; i < FeatureNum; i++)
{
DataRow dr = dt.NewRow();
dr[0] = FeatureName[i];
for (int j = 1; j < SampleNum + 1; j++)
{
dr[j] = app.CountMatrix[i, j - 1];
}
if (pvalue[i] == 100)
{
dr[3] = DBNull.Value;
dr[4] = DBNull.Value;
dr[5] = DBNull.Value;
}
else
{
dr[3] = pvalue[i];
dr[4] = bonferroni[i];
dr[5] = fdr[i];
}
if (this.checkBox1.Checked)
{
dr[SampleNum + 4] = Annotation[i];
}
else
{
dr[SampleNum + 4] = null;
}
for (int j = 0; j < SampleNum; j++)
{
dr[j + SampleNum + 5] = app.FreqMatrix[i, j];
}
dt.Rows.Add(dr);
}
DataTable dtCopy = dt.Copy();
DataTable dttemp = dt.Copy();
dttemp.Clear();
DataView dv = dt.DefaultView;
dv.Sort = "p.value";
dtCopy = dv.ToTable();
for (int i = 0; i < NAnum; i++)
{
DataRow row = dtCopy.Rows[i];
dttemp.Rows.Add(row.ItemArray);
}
for (int i = 0; i < NAnum; i++)
{
dtCopy.Rows.RemoveAt(0);
}
Microsoft.Office.Interop.Excel.Application xlApp = new Microsoft.Office.Interop.Excel.Application();
System.Globalization.CultureInfo CurrentCI = System.Threading.Thread.CurrentThread.CurrentCulture;
System.Threading.Thread.CurrentThread.CurrentCulture = new System.Globalization.CultureInfo("en-US");
Microsoft.Office.Interop.Excel.Workbooks workbooks = xlApp.Workbooks;
Microsoft.Office.Interop.Excel.Workbook workbook = workbooks.Add(Microsoft.Office.Interop.Excel.XlWBATemplate.xlWBATWorksheet);
Microsoft.Office.Interop.Excel.Worksheet worksheet = (Microsoft.Office.Interop.Excel.Worksheet)workbook.Worksheets[1];
Microsoft.Office.Interop.Excel.Range range;
long totalCount = dtCopy.Rows.Count;
long rowRead = 0;
float percent = 0;
for (int i = 0; i < dtCopy.Columns.Count - SampleNum; i++)
{
worksheet.Cells[1, i + 1] = dtCopy.Columns[i].ColumnName;
range = (Microsoft.Office.Interop.Excel.Range)worksheet.Cells[1, i + 1];
range.Interior.ColorIndex = 15;
range.Font.Bold = true;
}
for (int r = 0; r < dtCopy.Rows.Count; r++)
{
for (int i = 0; i < dtCopy.Columns.Count - SampleNum; i++)
{
worksheet.Cells[r + 2, i + 1] = dtCopy.Rows[r][i].ToString();
}
rowRead++;
percent = ((float)(100 * rowRead)) / totalCount;
}
xlApp.Visible = true;
double[,] df = new double[Math.Min(10, FeatureNum), SampleNum];
for (int i = 0; i < Math.Min(10, FeatureNum); i++)
{
for (int j = 0; j < SampleNum; j++)
{
df[i, j] = double.Parse(dtCopy.Rows[i][SampleNum + 5 + j].ToString());
}
}
string[] rownames = new string[Math.Min(10, FeatureNum)];
for (int i = 0; i < Math.Min(10, FeatureNum); i++)
{
rownames[i] = dtCopy.Rows[i][0].ToString();
}
CharacterVector Rrownames = TSS.CreateCharacterVector(rownames);
TSS.SetSymbol("Rowname", Rrownames);
NumericMatrix Rdf = TSS.CreateNumericMatrix(df);
TSS.SetSymbol("Freqdf", Rdf);
NumericVector RRow = TSS.CreateNumeric(Math.Min(10, FeatureNum));
TSS.SetSymbol("selrow", RRow);
TSS.Evaluate("Freqdf <- as.data.frame(Freqdf)");
TSS.Evaluate("rownames(Freqdf) <- Rowname");
TSS.Evaluate("colnames(Freqdf) <- SampleName");
TSS.Evaluate("colournum <- rainbow(dim(Freqdf)[2])");
TSS.Evaluate("plotdata <- t(Freqdf)");
TSS.Evaluate("windows()");
TSS.Evaluate("barplot(plotdata,main=\"features with top varition\",ylab=\"Freq\",beside=TRUE,horiz=FALSE, cex.names=0.6,col=colournum)");
TSS.Evaluate("legend(\"topright\",SampleName,fill=colournum)");
}
else
{
MessageBox.Show("Sample number is more than two!!");
}
this.Close();
}
