R/counts2Venn.R

In jtlovell/physGenomicsPVFinal: Differential Gene Expression for several Switchgrass Projects

counts2Venn<-function(x, cols, names, colors=c("darkblue","green","cyan","darkred"), ...){

  require(venneuler, warn.conflicts = FALSE, quietly=TRUE)

  mat<-as.matrix(x[,cols])
  colnames(mat)<-names
  cs<-apply(mat,2, function(x) sum(x!=0))
  c2<-lapply(data.frame(combn(colnames(mat),m=2)),function(x) as.vector(x))
  if(length(names)>1){
    cs2<-sapply(c2, function(x) {
      temp<-mat[,x]
      sum(temp[,1]!=0 & temp[,2]!=0)
    })
    names(cs2)<-sapply(c2, function(x) paste(x, collapse="_"))
  }else{
    cs2<-""
  }
  if(length(names)>2){
    c3<-lapply(data.frame(combn(colnames(mat),m=3)),function(x) as.vector(x))
    cs3<-sapply(c3, function(x) {
      temp<-mat[,x]
      sum(temp[,1]!=0 & temp[,2]!=0 & temp[,3]!=0)
    })
    names(cs3)<-sapply(c3, function(x) paste(x, collapse="_"))
  }else{
    cs3<-""
  }
  if(length(names)>3){
    c4<-lapply(data.frame(combn(colnames(mat),m=4)),function(x) as.vector(x))
    cs4<-sapply(c4, function(x) {
      temp<-mat[,x]
      sum(temp[,1]!=0 & temp[,2]!=0 & temp[,3]!=0 & temp[,4]!=0)
    })
    names(cs4)<-sapply(c4, function(x) paste(x, collapse="_"))
  }else{
    cs4<-""
  }
  cs<-paste(paste(names(cs), cs, sep="="), collapse="  ")
  cs2<-paste(paste(names(cs2), cs2, sep="="), collapse="  ")
  cs3<-paste(paste(names(cs3), cs3, sep="="), collapse="  ")
  cs4<-paste(paste(names(cs4), cs4, sep="="), collapse="  ")
  plot(v <- venneuler(mat != 0, colors), col=colors,
       sub=paste(cs,"\n",cs2,"\n",cs3,"\n",cs4), cex.sub=.8, ...)
}