R/conClust.R

In shaoqiangzhang/SCENA: Consensus clustering of single-cell RNA-seq data by enhancing network affinity

consClust<-function(Express=Express,num=num){
  library(SNFtool)
  group1=read.table("./data1.txt",header = T,quote = "",sep=' ')
  group2=read.table("./data2.txt",header = T,quote = "",sep=' ')
  group3=read.table("./data3.txt",header = T,quote = "",sep=' ')
  group4=read.table("./data4.txt",header = T,quote = "",sep=' ')
  group5=read.table("./data5.txt",header = T,quote = "",sep=' ')
 # file.remove("./data1.txt")
  #file.remove("./data2.txt")
  #file.remove("./data3.txt")
  #file.remove("./data4.txt")
  #file.remove("./data5.txt")
  group1=t(group1)
  group2=t(group2)
  group3=t(group3)
  group4=t(group4)
  group5=t(group5)
  a1=max(group1)
  a2=max(group2)
  a3=max(group3)
  a4=max(group4)
  a5=max(group5)
  #Merge the results
  tt=result(Express,group1,group2,group3,group4,group5)
  if(missing(num)==TRUE){
    c1=c(a1,a2,a3,a4,a5)
    c1=median(c1)
    res=spectralClustering(tt, c1)
  }
  else
    res=spectralClustering(tt, num)

  cat("Cluster label:\n")
  print(res)
  return(res)
}