diff --git a/AverageNetwork3.R b/AverageNetwork3.R
new file mode 100644
index 0000000..ce69116
--- /dev/null
+++ b/AverageNetwork3.R
@@ -0,0 +1,553 @@
+#source("/home/zgong001/Documents/Alarm/D50C9v/RCode/CombineOrders.R")
+getRelation = 
+  function(st = "[6][8][5][7|6:8:5][1|7][3|7:1][4|1][2|4][0|2]"){
+    re = c()
+    temstr = substr(st, 2, nchar(st)-1)
+    stlist = strsplit(chartr(old = "][", new = "##", temstr), "##")
+    for(i in 1:length(stlist[[1]])){
+      temc = chartr(old = "|", new = "g", stlist[[1]][i])
+      
+      if (grepl("g", temc)){
+        temc2 = strsplit(temc, "g")
+        
+        X = temc2[[1]][1]
+        TY = strsplit(temc2[[1]][2], ":")
+        for(j in 1:length(TY[[1]])){
+          Y = TY[[1]][j]
+          
+          cc= paste(Y,"->", X, sep = "")
+          re = append(re, cc)
+        }
+      }
+    }
+    return(re)
+  }
+
+creatDataframe = 
+  function(v = c("0", "1","2","3","4","5","6","7","8"), r = 246){
+    cn = c()
+    co= combn(v,2)
+    for(i in 1:ncol(co)){
+      X = co[1,i]
+      Y = co[2,i]
+      c1 = paste(X, "->", Y, sep = "")
+      cn = append(cn,c1)
+      c2 = paste(Y, "->", X, sep = "")
+      cn = append(cn,c2)
+      c3 = paste(X, " NA ", Y, sep = "")
+      cn = append(cn,c3)
+    }
+    
+    b= ncol(co)
+    
+    re = data.frame(matrix(0, nrow=r, ncol=b*3))
+    colnames(re) = cn
+    
+    return(re)
+  }
+
+#---------------------------------------------------------------------------------
+sortStru = function(st = "[5][6][8][7|5:8][1|5:7][3|7:8][2|6:1][4|1][0|2]"){
+  library(dplyr)
+  re = ""
+  temstr = substr(st, 2, nchar(st)-1)
+  stlist = strsplit(chartr(old = "][", new = "##", temstr), "##")
+  stlist = sort(stlist[[1]])
+  for(i in 1:length(stlist)){
+    if(nchar(stlist[i])>3){
+      
+      temc = chartr(old = "|", new = "g", stlist[i])
+      
+      temc2 = strsplit(temc, "g")
+      X = temc2[[1]][1]
+      TY = strsplit(temc2[[1]][2], ":")
+      TY = sort(TY[[1]])
+      
+      TY2 = paste(TY, collapse = ":")
+      
+      stlist[i] = paste(X,"|", TY2, sep = "")
+      
+      stlist[i] <- TY %>%
+        paste(., collapse=":") %>%
+        paste(X, "|", ., sep = "") 
+      
+    }
+    
+  }
+  
+  re <- stlist %>%
+    paste(., collapse="][") %>%
+    paste("[", ., "]", sep = "") 
+  
+  return(re)
+}
+
+MB = 
+  function (struc ="[6][8][5][7|6:8:5][3|7][1|7:3][4|1][2|4][0|2]", v ="1"){
+    
+    library(xlsx)
+    library(bnlearn)
+    library(dplyr)
+    
+    
+    mbs = ""
+    
+    strutem <- struc %>%
+      as.character(.) %>%
+      substr(., 2, nchar(.)-1) 
+    
+    stru =  strsplit(chartr(old = "][", new = "##", strutem), "##")
+    
+    for(j in 1:length(stru[[1]])){
+      if(grepl(v,stru[[1]][j])){
+        mbs = paste(mbs, "[", stru[[1]][j], "]", sep = "")
+      }
+    }
+    return(mbs)
+  }
+
+sumTable = 
+  function (pathname = "/home/zgong001/Documents/Alarm/D1KC9v/D1KC9v BestOrders/Strus_D1KC9v.txt", 
+            t = c("B-W",	"AIFM1",	"ATP6V1C2",	"CACNA1D",	"CACNB1",	"CDH15",	"CLDN6",	"DDIT3",	"EIF2AK3",	"ENDOG",	"HRK",	
+                  "LMNB1"	,"MAPK12",	"NRF1",	"PARP1"	,"PCK2",	"PLA2G4C",	"PPP2R3B",	"VDAC2",	"VDAC3"), 
+            exfilename = "/home/zgong001/Documents/Alarm/D1KC9v/D1KC9v BestOrders/Strus_D1KC9v.xlsx"){
+    library(bnlearn)
+    library(xlsx)
+    library(dplyr)
+    
+    v = as.character(seq(0,length(t)-1),1)
+    suminput = read.table(pathname, header = FALSE)
+    suminput = na.omit(suminput)
+    sumResu = data.frame()
+    n = ncol(suminput)
+    ord = vector()
+    
+    for(l in 1:nrow(suminput)){
+      tem = suminput[l,1]
+      for(m in 2:(n-4)){
+        tem = paste(tem, suminput[l,m], sep = " ")
+      }
+      ord = append(ord, tem)
+    }
+    
+    
+    suminput = cbind(suminput, ord)
+    
+    
+    suminput = suminput[-n]
+    
+    for(j in (n-4):1){
+      suminput = suminput[,-j]
+    }
+    
+    colnames(suminput)[1] <- "OrderScores"
+    colnames(suminput)[2] <- "Structures"
+    colnames(suminput)[3] <- "StructScores"
+    
+    orders= aggregate( OrderScores ~ord, data=suminput, FUN = mean)
+    orders = orders[order(-orders[,2]), ]
+    for(i in 1:nrow(orders)){
+      orders$Opercentage[i] = exp(-log(sum(exp(orders$OrderScores-orders$OrderScores[i]))))
+    }
+    
+    orders$Ocumper = cumsum(orders$Opercentage)
+    
+    for(i in 1:nrow(orders)){
+      tem = suminput[which(suminput$ord== orders[i,1]), ]
+      
+      tem$Opercentage = orders[i,3]
+      tem$Ocumper = orders[i,4]
+      
+      for(j in 1:nrow(tem)){
+        tem$Spercentage[j] = exp(-log(sum(exp(tem$StructScores-tem$StructScores[j]))))
+      }
+      tem$Scumper = cumsum(tem$Spercentage)
+      tem = tem[c("ord", "OrderScores", "Opercentage","Ocumper", "Structures", "StructScores","Spercentage","Scumper")]
+      sumResu = rbind(sumResu, tem)
+    }
+    
+    
+    for(k in 1:nrow(sumResu)){
+      sumResu$sortS[k] = sortStru(as.character(sumResu$Structures[k]))
+    }
+    
+    rs = nrow(sumResu)
+    
+    rl = creatDataframe(v,rs)
+    sumResu= cbind(sumResu, rl)
+    
+    #    sumAnce = sumResu
+    
+    co= combn(v,2)
+    
+    for(i in 1:nrow(sumResu)){
+      s = as.character(sumResu [i,5])
+      rel = getRelation(st = s)
+      
+      for(j in 1:ncol(co)){
+        X = co[1,j]
+        Y = co[2,j]
+        c1 = paste(X, "->", Y, sep = "")
+        c2 = paste(Y, "->", X, sep = "")
+        c3 = paste(X, " NA ", Y, sep = "")
+        
+        if (c1 %in% rel){
+          sumResu[i,c1] = sumResu$Opercentage[i]*sumResu$Spercentage[i]
+        }
+        else if(c2 %in% rel){
+          sumResu[i,c2] = sumResu$Opercentage[i]*sumResu$Spercentage[i]
+        }
+        else{
+          sumResu[i,c3] = sumResu$Opercentage[i]*sumResu$Spercentage[i]
+        }
+        
+      }
+      
+    }
+    
+    #    print(sumResu)
+    
+    sumP = colSums(sumResu[, -c(1:9)])
+    
+    #    print (sumP)
+    
+    ##########################################
+    
+    
+    
+    StruWithO = aggregate( StructScores ~sortS, data=sumResu, FUN = mean)
+    
+    for(l in 1:nrow(StruWithO)){
+      StruWithO$Spercentage[l] = exp(-log(sum(exp(StruWithO$StructScores-StruWithO$StructScores[l]))))
+    }
+    
+    StruWithO = StruWithO[order(-StruWithO[,3]), ]
+    
+    rss = nrow(StruWithO)
+    
+    rls = creatDataframe(v,rss)
+    StruWithO= cbind(StruWithO, rls)
+    
+    for(m in 1:nrow(StruWithO)){
+      ss = as.character(StruWithO [m,1])
+      rels = getRelation(st = ss)
+      #      print(rels)
+      
+      for(n in 1:ncol(co)){
+        X = co[1,n]
+        Y = co[2,n]
+        c1 = paste(X, "->", Y, sep = "")
+        c2 = paste(Y, "->", X, sep = "")
+        c3 = paste(X, " NA ", Y, sep = "")
+        
+        if (c1 %in% rels){
+          StruWithO[m,c1] = StruWithO$Spercentage[m]
+        }
+        else if(c2 %in% rels){
+          StruWithO[m,c2] = StruWithO$Spercentage[m]
+        }
+        else{
+          StruWithO[m,c3] = StruWithO$Spercentage[m]
+        }
+        
+      }
+      
+    }
+    
+    
+    sumpS = colSums(StruWithO[, -c(1:3)])
+    #    print(sumpS)
+    
+    #    totS = (sumP+sumpS)/2
+    
+    #    nam = names(totS)
+    nam = names(sumP)
+    
+    #    nam2 = names(sumpS)
+    
+    #    print(nam2)
+    
+    for(i in 1:length(nam)){
+      if (grepl("->", nam[i])){
+        TY = strsplit(nam[i], "->")
+        a = as.numeric(TY[[1]][1])
+        b = as.numeric(TY[[1]][2])
+        nam[i] = paste(t[a+1], "->", t[b+1], sep = "")
+      }
+      
+      if (grepl(" NA ", nam[i])){
+        TY = strsplit(nam[i], " NA ")
+        a = as.numeric(TY[[1]][1])
+        b = as.numeric(TY[[1]][2])
+        nam[i] = paste(t[a+1], " NA ", t[b+1], sep = "")
+      }
+      
+    }
+    
+    #    print(nam)
+    names(sumP) = nam
+    names(sumpS) = nam
+    
+    sumP = as.data.frame(sumP)
+    sumpS = as.data.frame(sumpS)
+    
+    #     print(sumP)
+    
+    #    print(totS)
+    
+    write.xlsx(sumP, exfilename, sheetName = "Pairs", col.names = TRUE, row.names = TRUE, append = FALSE)
+    write.xlsx(sumpS, exfilename, sheetName = "Pairs-WO", col.names = TRUE, row.names = TRUE, append = TRUE)
+    
+    #    return(sumpS)
+    
+  }
+
+
+
+AverageNet = function(pathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx",
+                      outfile = "/home/zgong001/Documents/dot/out.gv"){
+  
+  library(xlsx)
+  
+  res <- read.xlsx(pathname, 1)  # read first sheet
+  res = na.omit(res)
+  
+  cat("digraph G {", file=outfile, sep="\n")
+  
+  p = round(nrow(res)/3)
+  
+  for(i in 1:p){
+    
+    t = (i-1)*3
+    v = as.vector(res[(t+1):(t+3),2])
+    names(v) = res[(t+1):(t+3),1]
+    m = sort(v, decreasing = TRUE)
+    mn = names(m[1])
+    if(grepl("->", mn)){
+      if(grepl("->", names(m[2]))){
+        cat("\t", mn, " [penwidth=", round(m[[1]]*2,digits = 2), ",", 'label="', round(m[[1]]*100 ,digits = 2), " (", round(m[[2]]*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+      }
+      else{
+        cat("\t", mn, " [penwidth=", round(m[[1]]*2,digits = 2), ",", 'label="', round(m[[1]]*100,digits = 2) , " (", round(m[[3]]*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+      }
+      
+    }
+    
+  }
+  
+  cat("}", file=outfile, append=TRUE)
+  return(res)
+}
+
+############This is draw pairs percent on the graph.
+AverageNet11 = function(pathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx",
+                       str = "",
+                       outfile = "/home/zgong001/Documents/dot/out.gv"){
+  
+  library(xlsx)
+  library(bnlearn)
+  
+  res <- read.xlsx(pathname, 1)  # read first sheet
+  res = na.omit(res)
+  
+  strD = model2network(as.character(str))
+  arcD = arcs(strD)
+  nodeD = nodes(strD)
+  arNo = unique(union(arcD[,1], arcD[,2]))
+  nod = setdiff(nodeD, arNo)
+  
+  cat("digraph G {", file=outfile, sep="\n")
+  
+  if (length(nod) > 0){
+    for(j in 1:length(nod)){
+      cat("\t", nod[j], "\n", file=outfile, append=TRUE)
+    }
+  }
+  
+  p = nrow(arcD)
+  
+  for(i in 1:p){
+    
+    mn = paste(arcD[i,1],"->" , arcD[i,2], sep = "")
+    mn2 = paste(arcD[i,2],"->" , arcD[i,1], sep = "")
+    s1 = res[which(res[,1]==mn),2]
+    s2 = res[which(res[,1]==mn2),2]
+    
+    if((s1>=0.9999)&(s2<=0.0001)){
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+      
+    } else if (s1>=0.9999) {
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+      
+    } else if (s2<=0.0001) {
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+      
+    } else {
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+    }
+    
+    
+  }
+  
+  cat("\t", 'label="', '      ', "\\l", "Notes:", "\\l", "    -   >99 represents percentage of 99.99 and above", "\\l", "    -   ~0  represents percentage of 0.01 and below", "\\l", "    -   Percentage in the parentheses represents the percentage of an arc that is reversed", '\\l"', ";", "\n", file=outfile, append=TRUE)
+  cat("}", file=outfile, append=TRUE)
+  return(res)
+}
+
+ExeAve = function(epathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx",
+                  strfile = "",
+                  outfile = "/home/zgong001/Documents/dot/"){
+  library(xlsx)
+  strs =  read.xlsx(strfile, sheetName = "Structures")  # read first sheet
+  strs = na.omit(strs)
+  strs = as.data.frame(strs[1:2,1])
+  
+  
+  for(i in 1:2){
+    oun = paste(outfile, "-", i, ".gv", sep = "")
+    y = AverageNet11(pathname = epathname,
+                    str = as.character(strs[i,1]),
+                    outfile = oun)
+  }
+  
+  return (strs)
+  
+}
+
+##################################################################################################################
+# The following is for the Consensus version 2
+AverageNet21 = function(pathname = "/home/zgong001/Documents/Projects/Luminal/3/SS/Pairs-A3-Luminal A-A-B.xlsx",
+                         str = "",
+                         outfile = "/home/zgong001/Documents/dot/out.gv"){
+  
+  library(xlsx)
+  library(bnlearn)
+  
+  res <- read.xlsx(pathname, 1)  # read first sheet
+  res = na.omit(res)
+  
+  
+  
+  strD = model2network(as.character(str))
+  arcD = arcs(strD)
+  nodeD = nodes(strD)
+  arNo = unique(union(arcD[,1], arcD[,2]))
+  nod = setdiff(nodeD, arNo)
+  
+  cat("digraph G {", file=outfile, sep="\n")
+  
+  if (length(nod) > 0){
+    for(j in 1:length(nod)){
+      cat("\t", nod[j], "\n", file=outfile, append=TRUE)
+    }
+  }
+  
+  p = nrow(arcD)
+  
+  for(i in 1:p){
+    
+    mn = paste(arcD[i,1],"->" , arcD[i,2], sep = "")
+    mn2 = paste(arcD[i,2],"->" , arcD[i,1], sep = "")
+    s1 = res[which(res[,1]==mn),2]
+    s2 = res[which(res[,1]==mn2),2]
+    
+    if((s1>=0.9999)&(s2<=0.0001)){
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+      
+    } else if (s1>=0.9999) {
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', ">99", " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+      
+    } else if (s2<=0.0001) {
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+      
+    } else {
+      
+      cat("\t", mn, " [penwidth=", round(s1*10, digits = 2), ",", 'label="', round(s1*100 ,digits = 2), " (", round(s2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+      
+    }
+    
+    
+    
+  }
+  
+  NoNA = data.frame()
+  
+  arcD = as.data.frame(arcD)
+  co= combn(nodeD,2)
+  
+  
+  for(j in 1:ncol(co)){
+    X = co[1,j]
+    Y = co[2,j]
+    
+    pair_find1 = data.frame(from= X, to=Y)
+    pair_find2 = data.frame(from= Y, to=X)
+    
+    if((nrow(merge(pair_find1,arcD )) == 0) & (nrow(merge(pair_find2,arcD )) == 0)){
+      
+      TX = paste(X,"->", Y, sep = "")
+      TY = paste(Y,"->", X, sep = "")
+      t1 = res[which(res[,1]==TX),2]
+      t2 = res[which(res[,1]==TY),2]
+      if(t1>t2){
+        
+        if((t1>=0.9999)&(t2<=0.0001)){
+          
+          cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+          
+        } else if (t1>=0.9999) {
+          
+          cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', ">99", " (", round(t2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+          
+        } else if (t2<=0.0001) {
+          
+          cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', round(t1*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+          
+        } else {
+          
+          cat("\t", TX, " [penwidth=", round(t1*10, digits = 2), ",", 'label="', round(t1*100 ,digits = 2), " (", round(t2*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+          
+        }
+        
+      }
+      else if (t2 >t1){
+        
+        if((t2>=0.9999)&(t1<=0.0001)){
+          
+          cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', ">99", " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+          
+        } else if (t2>=0.9999) {
+          
+          cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', ">99", " (", round(t1*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+          
+        } else if (t1<=0.0001) {
+          
+          cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', round(t2*100 ,digits = 2), " (", "~0",')"', "];", "\n", file=outfile, append=TRUE)
+          
+        } else {
+          
+          cat("\t", TY, " [penwidth=", round(t2*10, digits = 2), ",", 'label="', round(t2*100 ,digits = 2), " (", round(t1*100,digits = 2),')"', "];", "\n", file=outfile, append=TRUE)
+          
+        }
+        
+      }
+      else{
+        next
+      }
+      
+      
+    }
+    
+    
+  }
+  
+  cat("\t", 'label="', '      ', "\\l", "Notes:", "\\l", "    -   >99 represents percentage of 99.99 and above", "\\l", "    -   ~0  represents percentage of 0.01 and below", "\\l", "    -   Percentage in the parentheses represents the percentage of an arc that is reversed", '\\l"', ";", "\n", file=outfile, append=TRUE)
+  cat("}", file=outfile, append=TRUE)
+  return(arcD)
+}
\ No newline at end of file