private void gTwoGroupsOfSamplesStaticsToolStripMenuItem_Click(object sender, EventArgs e)
{
Two_Groups_Ana TwoGroupsTest = new Two_Groups_Ana();
TwoGroupsTest.MdiParent = this;
TwoGroupsTest.Show();
}
private void button4_Click(object sender, EventArgs e)
{
if (this.textBox3.Text == "")
{
MessageBox.Show("Please enter the sample number of Group I!", "WARNIMG");
Two_Groups_Ana TwoGroupsTest = new Two_Groups_Ana();
TwoGroupsTest.MdiParent = this.MdiParent;
TwoGroupsTest.Show();
this.Close();
}
else
{
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;
REngine.SetEnvironmentVariables();
REngine TGS = REngine.GetInstance();
TGS.Initialize();
NumericMatrix Freq = TGS.CreateNumericMatrix(app.FreqMatrix);
TGS.SetSymbol("Freq", Freq);
NumericMatrix Count = TGS.CreateNumericMatrix(app.CountMatrix);
TGS.SetSymbol("Count", Count);
NumericVector RFeatureNum = TGS.CreateNumeric(FeatureNum);
NumericVector RSampleNum = TGS.CreateNumeric(SampleNum);
TGS.SetSymbol("FeatureNum", RFeatureNum);
TGS.SetSymbol("SampleNum", RSampleNum);
CharacterVector SampleName = TGS.CreateCharacterVector(app.SamName);
CharacterVector FeatureName = TGS.CreateCharacterVector(app.FeaName);
TGS.SetSymbol("FeatureName", FeatureName);
TGS.SetSymbol("SampleName", SampleName);
List <string> SampleNameFreq = new List <string>();
List <double?> OddRatio = new List <double?>();
List <double?> absOddRatio = new List <double?>();
List <List <double> > Freqtemp = new List <List <double> >();
List <double> FreqSum = new List <double>();
int Correct1 = 0;
int Correct2 = 0;
int method = 0;
int GroupNum = int.Parse(this.textBox3.Text.ToString());
NumericVector RGroupNum = TGS.CreateNumeric(GroupNum);
TGS.SetSymbol("Groupsep", RGroupNum);
for (int i = 0; i < SampleNum; i++)
{
SampleNameFreq.Add(SampleName[i] + "Freq");
}
if (this.comboBox1.SelectedIndex == 0)
{
int effNum1, effNum2;
TGS.Evaluate("FeatureSums1 <- rowSums(Count[,1:Groupsep])");
TGS.Evaluate("FeatureSums2 <- rowSums(Count[,Groupsep:SampleNum])");
TGS.Evaluate("effnum1 <- length(FeatureSums1[FeatureSums1 > Groupsep])");
TGS.Evaluate("effnum2 <- length(FeatureSums2[FeatureSums2 > (SampleNum - Groupsep)])");
effNum1 = Convert.ToInt32(TGS.GetSymbol("effnum1").AsNumeric().First());
effNum2 = Convert.ToInt32(TGS.GetSymbol("effnum2").AsNumeric().First());
for (int i = 0; i < FeatureNum; i++)
{
double rowsums1 = 0;
double rowsums2 = 0;
double[] rowsCount1 = new double[GroupNum];
for (int j = 0; j < GroupNum; j++)
{
rowsums1 = rowsums1 + app.CountMatrix[i, j];
rowsCount1[j] = app.CountMatrix[i, j];
}
if (rowsums1 > GroupNum)
{
NumericVector rowscount1 = TGS.CreateNumericVector(rowsCount1);
TGS.SetSymbol("rowcount1", rowscount1);
TGS.Evaluate("result1 <- ks.test(rowcount1,\"pnorm\",mean(rowcount1),sd(rowcount1))");
TGS.Evaluate("factor1 <- result1$p");
double prows1 = TGS.GetSymbol("factor1").AsNumeric().First();
if (prows1 < 0.05)
{
Correct1 = Correct1 + 1;
}
}
double[] rowsCount2 = new double[SampleNum - GroupNum];
for (int j = GroupNum; j < SampleNum; j++)
{
rowsums2 = rowsums2 + app.CountMatrix[i, j];
rowsCount2[j - GroupNum] = app.CountMatrix[i, j];
}
if (rowsums2 > (SampleNum - GroupNum))
{
NumericVector rowscount2 = TGS.CreateNumericVector(rowsCount2);
TGS.SetSymbol("rowcount2", rowscount2);
TGS.Evaluate("result2 <- ks.test(rowcount2,\"pnorm\",mean(rowcount2),sd(rowcount2))");
TGS.Evaluate("factor2 <- result2$p");
double prows2 = TGS.GetSymbol("factor2").AsNumeric().First();
if (prows2 < 0.05)
{
Correct2 = Correct2 + 1;
}
}
}
bool condition1 = (Correct1 >= effNum1 * 0.5) && (Correct2 >= effNum2 * 0.5);
bool condition2 = GroupNum == SampleNum - GroupNum;
if (condition1)
{
if (condition2)
{
method = 2;
}
else
{
method = 1;
}
}
else
{
if (condition2)
{
method = 4;
}
else
{
method = 3;
}
}
switch (method)
{
case 1:
MessageBox.Show("Statistical Method : t-test");
break;
case 2:
MessageBox.Show("Statistical Method : Pair t-test");
break;
case 3:
MessageBox.Show("Statistical Method : Mann-Whitney U test");
break;
case 4:
MessageBox.Show("Statistical Method : Wilcoxon sign-rank test");
break;
default:
break;
}
}
TGS.Evaluate("FreqMatrix <- as.data.frame(Freq)");
TGS.Evaluate("names(FreqMatrix) <- SampleName");
TGS.Evaluate("samp1_mean <- apply(FreqMatrix[,1:Groupsep],1,mean)");
TGS.Evaluate("samp2_mean <- apply(FreqMatrix[,(Groupsep+1):SampleNum],1,mean)");
TGS.Evaluate("samp1_sd <- apply(FreqMatrix[,1:Groupsep],1,sd)");
TGS.Evaluate("samp2_sd <- apply(FreqMatrix[,(Groupsep+1):SampleNum],1,sd)");
TGS.Evaluate("samp1_stat <- paste(samp1_mean,samp1_sd,sep=\"±\")");
TGS.Evaluate("samp2_stat <- paste(samp2_mean,samp2_sd,sep=\"±\")");
string[] s1_stat = (string[])TGS.GetSymbol("samp1_stat").AsCharacter().ToArray();
string[] s2_stat = (string[])TGS.GetSymbol("samp2_stat").AsCharacter().ToArray();
if (this.comboBox1.SelectedIndex != 6)
{
switch (this.comboBox1.SelectedIndex + method)
{
case 1:
for (int i = 1; i <= FeatureNum; i++)
{
TGS.SetSymbol("i", TGS.CreateNumeric(i));
TGS.Evaluate("group1_freq <- as.numeric(FreqMatrix[i,1:Groupsep])");
TGS.Evaluate("group2_freq <- as.numeric(FreqMatrix[i,(Groupsep+1):SampleNum])");
TGS.Evaluate("p.value <- t.test(group1_freq,group2_freq, paired=FALSE)$p.value");
pvalue.Add(TGS.GetSymbol("p.value").AsNumeric().First());
}
break;
case 2:
if (GroupNum != SampleNum - GroupNum)
{
MessageBox.Show("This statistical test must have same number samples in each category!", "WARNIMG");
break;
}
else
{
for (int i = 1; i <= FeatureNum; i++)
{
TGS.SetSymbol("i", TGS.CreateNumeric(i));
TGS.Evaluate("group1_freq <- as.numeric(FreqMatrix[i,1:Groupsep])");
TGS.Evaluate("group2_freq <- as.numeric(FreqMatrix[i,(Groupsep+1):SampleNum])");
TGS.Evaluate("p.value <- t.test(group1_freq,group2_freq, paired=TRUE)$p.value");
pvalue.Add(TGS.GetSymbol("p.value").AsNumeric().First());
}
break;
}
case 3:
for (int i = 1; i <= FeatureNum; i++)
{
TGS.SetSymbol("i", TGS.CreateNumeric(i));
TGS.Evaluate("group1_freq <- as.numeric(FreqMatrix[i,1:Groupsep])");
TGS.Evaluate("group2_freq <- as.numeric(FreqMatrix[i,(Groupsep+1):SampleNum])");
TGS.Evaluate("p.value <- wilcox.test(group1_freq,group2_freq,exact = FALSE)$p.value");
pvalue.Add(TGS.GetSymbol("p.value").AsNumeric().First());
}
break;
case 4:
if (GroupNum != SampleNum - GroupNum)
{
MessageBox.Show("This statistical test must have same number samples in each category!", "WARNIMG");
break;
}
else
{
for (int i = 1; i <= FeatureNum; i++)
{
TGS.SetSymbol("i", TGS.CreateNumeric(i));
TGS.Evaluate("group1_freq <- as.numeric(FreqMatrix[i,1:Groupsep])");
TGS.Evaluate("group2_freq <- as.numeric(FreqMatrix[i,(Groupsep+1):SampleNum])");
TGS.Evaluate("p.value <- wilcox.test(group1_freq,group2_freq,paired=TRUE,exact = FALSE)$p.value");
pvalue.Add(TGS.GetSymbol("p.value").AsNumeric().First());
}
break;
}
case 5:
double Sum1 = 0;
double Sum2 = 0;
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < GroupNum; j++)
{
Sum1 = Sum1 + app.CountMatrix[i, j];
}
for (int j = GroupNum; j < SampleNum; j++)
{
Sum2 = Sum2 + app.CountMatrix[i, j];
}
}
for (int i = 0; i < FeatureNum; i++)
{
double n11 = 0;
double n12 = 0;
double n21 = 0;
double n22 = 0;
for (int j = 0; j < GroupNum; j++)
{
n11 = n11 + app.CountMatrix[i, j];
}
for (int j = GroupNum; j < SampleNum; j++)
{
n21 = n21 + app.CountMatrix[i, j];
}
n12 = Sum1 - n11;
n22 = Sum2 - n21;
NumericVector Rn11 = TGS.CreateNumeric(n11);
NumericVector Rn21 = TGS.CreateNumeric(n21);
NumericVector Rn12 = TGS.CreateNumeric(n12);
NumericVector Rn22 = TGS.CreateNumeric(n22);
TGS.SetSymbol("n11", Rn11);
TGS.SetSymbol("n12", Rn12);
TGS.SetSymbol("n21", Rn21);
TGS.SetSymbol("n22", Rn22);
TGS.Evaluate("compare <- matrix(c(n11,n12,n21,n22),nr=2)");
TGS.Evaluate("p.value <- fisher.test(compare)$p.value");
pvalue.Add(TGS.GetSymbol("p.value").AsNumeric().First());
}
break;
default:
break;
}
NumericVector Rpvalue = TGS.CreateNumericVector(pvalue);
TGS.SetSymbol("p.value", Rpvalue);
TGS.Evaluate("NAnum = length(p.value[is.nan(p.value)])");
NAnum = Convert.ToInt32(TGS.GetSymbol("NAnum").AsNumeric().First());
TGS.Evaluate("bonferroni.p <- p.adjust(p.value,\"bonferroni\")");
TGS.Evaluate("fdr.p <- p.adjust(p.value,\"fdr\")");
for (int i = 0; i < FeatureNum; i++)
{
bonferroni[i] = TGS.GetSymbol("bonferroni.p").AsNumeric()[i];
fdr[i] = TGS.GetSymbol("fdr.p").AsNumeric()[i];
}
List <string> Annotation = new List <string>();
if (this.checkBox1.Checked)
{
if (this.radioButton1.Checked)
{
string strConnCOG;
strConnCOG = "Provider=Microsoft.ACE.OLEDB.12.0;" + "Data Source=" + System.Windows.Forms.Application.StartupPath + "/COG.xlsx" + ";" + "Extended Properties=\"Excel 12.0;HDR=YES;IMEX=1\"";
OleDbConnection OleConnCOG = new OleDbConnection(strConnCOG);
OleConnCOG.Open();
String sqlCOG = "SELECT * FROM [Sheet1$]";
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(SampleName[i], typeof(double));;
}
dt.Columns.Add("group1", typeof(string));
dt.Columns.Add("group2", typeof(string));
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; j++)
{
dr[j] = app.CountMatrix[i, j - 1];
}
dr[SampleNum + 1] = s1_stat[i];
dr[SampleNum + 2] = s2_stat[i];
if (double.IsNaN(pvalue[i]))
{
dr[SampleNum + 3] = DBNull.Value;
dr[SampleNum + 4] = DBNull.Value;
dr[SampleNum + 5] = DBNull.Value;
}
else
{
dr[SampleNum + 3] = pvalue[i];
dr[SampleNum + 4] = bonferroni[i];
dr[SampleNum + 5] = fdr[i];
}
if (this.checkBox1.Checked)
{
dr[SampleNum + 6] = Annotation[i];
}
else
{
dr[SampleNum + 6] = null;
}
for (int j = 0; j < SampleNum; j++)
{
dr[j + SampleNum + 7] = 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;
int pnum = 0;
for (int i = 0; i < FeatureNum; i++)
{
try
{
if (double.Parse(dtCopy.Rows[i][SampleNum + 3].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 + 7 + 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 = TGS.CreateCharacterVector(rownamesdf);
TGS.SetSymbol("Rownamedf", Rrownamesdf);
NumericMatrix Rdf = TGS.CreateNumericMatrix(df);
TGS.SetSymbol("Freqdf", Rdf);
NumericVector RRow = TGS.CreateNumeric(Math.Min(10, FeatureNum));
TGS.SetSymbol("selrow", RRow);
TGS.Evaluate("Freqdf <- as.data.frame(Freqdf)");
TGS.Evaluate("rownames(Freqdf) <- Rownamedf");
TGS.Evaluate("colnames(Freqdf) <- SampleName");
TGS.Evaluate("colournum <- rainbow(dim(Freqdf)[2])");
TGS.Evaluate("plotdata <- t(Freqdf)");
TGS.Evaluate("windows()");
TGS.Evaluate("barplot(plotdata,main=\"features with top varition\",ylab=\"Freq\",beside=TRUE,horiz=FALSE, cex.names=0.6,col=colournum)");
TGS.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 + 7 + j].ToString());
}
}
string[] rownamesall = new string[pnum];
for (int i = 0; i < pnum; i++)
{
rownamesall[i] = dtCopy.Rows[i][0].ToString();
}
CharacterVector Rrownamesall = TGS.CreateCharacterVector(rownamesall);
TGS.SetSymbol("Rownameall", Rrownamesall);
NumericMatrix Rdfall = TGS.CreateNumericMatrix(dfall);
TGS.SetSymbol("Freqdfall", Rdfall);
NumericVector RRowall = TGS.CreateNumeric(pnum);
TGS.SetSymbol("selrowall", RRowall);
TGS.Evaluate("Freqdfall <- as.data.frame(Freqdfall)");
TGS.Evaluate("rownames(Freqdfall) <- Rownameall");
TGS.Evaluate("colnames(Freqdfall) <- SampleName");
TGS.Evaluate("distance <- as.dist(1-abs(cor(Freqdfall)))");
if (this.checkBox3.Checked)
{
TGS.Evaluate("fit <- cmdscale(distance, eig=TRUE, k=2)");
TGS.Evaluate("x <- fit$points[,1]");
TGS.Evaluate("y <- fit$points[,2]");
TGS.Evaluate("minx <- min(x)");
TGS.Evaluate("miny <- min(y)");
TGS.Evaluate("maxx <- max(x)");
TGS.Evaluate("maxy <- max(y)");
TGS.Evaluate("randx <- maxx - minx");
TGS.Evaluate("randy <- maxy - miny");
TGS.Evaluate("llimx <- minx - randx/10");
TGS.Evaluate("hlimx <- maxx + randx/3");
TGS.Evaluate("llimy <- miny - randy/10");
TGS.Evaluate("hlimy <- maxy + randy/3");
TGS.Evaluate("windows()");
TGS.Evaluate("plot(x,y,xlab=\"Coordinate 1\",ylab=\"Coordinate 2\",main=\"MDS\", pch=c(rep(0,Groupsep),rep(1,(length(SampleName)-Groupsep))),col=c(rep(\"red\",Groupsep),rep(\"green\",(length(SampleName)-Groupsep))), type=\"p\",xlim = c(llimx,hlimx), ylim = c(llimy,hlimy))");
if (this.comboBox3.SelectedIndex == 0)
{
TGS.Evaluate("legend(\"topright\",colnames(Freqdfall),pch=c(rep(0,Groupsep),rep(1,(length(SampleName)-Groupsep))),col=c(rep(\"red\",Groupsep),rep(\"green\",(length(SampleName)-Groupsep))),cex = 0.8)");
}
else if (this.comboBox3.SelectedIndex == 1)
{
TGS.Evaluate("text(x,y,labels=SampleName,pos=4)");
}
}
if (this.checkBox4.Checked)
{
TGS.Evaluate("windows()");
TGS.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 = TGS.CreateCharacterVector(rownameshm);
TGS.SetSymbol("Rownamehm", Rrownameshm);
NumericMatrix Rdfhm = TGS.CreateNumericMatrix(dfhm);
TGS.SetSymbol("Freqdfhm", Rdfhm);
NumericVector RRowhm = TGS.CreateNumeric(Math.Min(500, Rownum));
TGS.SetSymbol("plotnum", RRowhm);
TGS.Evaluate("Freqdfhm <- as.data.frame(Freqdfhm)");
TGS.Evaluate("rownames(Freqdfhm) <- Rownamehm");
TGS.Evaluate("colnames(Freqdfhm) <- SampleName");
TGS.Evaluate("Freqdfhm <- as.matrix(Freqdfhm)");
TGS.Evaluate("library(pheatmap)");
TGS.Evaluate("windows()");
if (this.checkBox6.Checked)
{
if (this.checkBox7.Checked)
{
TGS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=T,cluster_rows=T)");
}
else
{
TGS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=F,cluster_rows=T)");
}
}
else
{
if (this.checkBox7.Checked)
{
TGS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=T,cluster_rows=F)");
}
else
{
TGS.Evaluate("pheatmap(Freqdfhm[1:plotnum,],show_rownames=F,cluster_rows=F)");
}
}
}
}
else if (this.comboBox1.SelectedIndex == 6)
{
double Sum1 = 0;
double Sum2 = 0;
for (int i = 0; i < FeatureNum; i++)
{
for (int j = 0; j < GroupNum; j++)
{
Sum1 = Sum1 + app.CountMatrix[i, j];
}
for (int j = GroupNum; j < SampleNum - 1; j++)
{
Sum2 = Sum2 + app.CountMatrix[i, j];
}
}
TGS.SetSymbol("Sum1", TGS.CreateNumeric(Sum1));
TGS.SetSymbol("Sum2", TGS.CreateNumeric(Sum2));
TGS.Evaluate("R <- Sum1/Sum2");
TGS.Evaluate("treatadd <- R/(R+1)");
TGS.Evaluate("controladd <- 1/(R+1)");
for (int i = 0; i < FeatureNum; i++)
{
double n11 = 0;
double n12 = 0;
double n21 = 0;
double n22 = 0;
for (int j = 0; j < GroupNum; j++)
{
n11 = n11 + app.Count[i][j];
}
for (int j = GroupNum; j < SampleNum - 1; j++)
{
n21 = n21 + app.Count[i][j];
}
if ((n11 < GroupNum) && (n21 < SampleNum - 1 - GroupNum))
{
OddRatio.Add(null);
absOddRatio.Add(null);
}
else
{
n12 = Sum1 - n11;
n22 = Sum2 - n21;
TGS.SetSymbol("n11", TGS.CreateNumeric(n11));
TGS.SetSymbol("n12", TGS.CreateNumeric(n12));
TGS.SetSymbol("n21", TGS.CreateNumeric(n21));
TGS.SetSymbol("n22", TGS.CreateNumeric(n22));
TGS.Evaluate("odd_ratio <- log2(((n11+treatadd)*(n22+controladd))/((n21+controladd)*(n12+treatadd )))");
OddRatio.Add(double.Parse(TGS.GetSymbol("odd_ratio").ToString()));
absOddRatio.Add(Math.Abs(double.Parse(TGS.GetSymbol("odd_ratio").ToString())));
}
}
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(SampleName[i], typeof(double));;
}
dt.Columns.Add("Odd_Ratio", typeof(double));
dt.Columns.Add("abs_Odd_Ratio", typeof(double));
dt.Columns.Add("Annotation", typeof(string));
for (int i = 0; i < FeatureNum; i++)
{
DataRow dr = dt.NewRow();
dr[0] = FeatureName[i];
for (int j = 1; j <= SampleNum; j++)
{
dr[j] = app.CountMatrix[i, j - 1];
}
if (OddRatio[i] == null)
{
dr[SampleNum] = DBNull.Value;
dr[SampleNum + 1] = DBNull.Value;
}
else
{
dr[SampleNum] = OddRatio[i];
dr[SampleNum + 1] = absOddRatio[i];
}
if (this.checkBox1.Checked)
{
dr[SampleNum + 2] = Annotation[i];
}
else
{
dr[SampleNum + 2] = null;
}
dt.Rows.Add(dr);
}
DataTable dtCopy = dt.Copy();
DataView dv = dt.DefaultView;
dv.Sort = "abs_Odd_Ratio DESC";
dtCopy = dv.ToTable();
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; 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; i++)
{
worksheet.Cells[r + 2, i + 1] = dtCopy.Rows[r][i].ToString();
}
rowRead++;
percent = ((float)(100 * rowRead)) / totalCount;
}
xlApp.Visible = true;
}
this.Close();
}
}
