Converts a hclust dendrogram into a graph in JSON for input into D3

DendToForce.R

#Run hclust
hc <- hclust(dist(USArrests[1:40,]), "ave")

#Function for extracting nodes and links
extractGraph<-function(hc){
  
  n<-length(hc$order)
  m<-hc$merge

  links<-data.frame(source=as.numeric(), target=as.numeric(), value=as.numeric())
  
  for (i in 1:(n-2)){
  
  #Deal with the different kinds of links
    #It's not working at the moment because the row numbers for the new nodes don't match the index in the node table
    #Will have to track their creation or post hoc adjust them
    #and/or because the when two new nodes combine they need to make another new node - in fact in all cases there needs to be another node
    
    n1<-m[i,1]
    n2<-m[i,2]
    
    if(n1<0 & n2<0) {links.add<-rbind(c(-n1-1, i+n-1, 1), c(-n2-1, i+n-1, 1))}
    
    else if (n1>0 & n2<0) {links.add<-rbind( c(n+n1-1,i+n-1, 1), c(-n2-1,i+n-1, 1)) }
    
    else if (n1<0 & n2>0) {links.add<-rbind( c(-n1-1,i+n-1, 1), c(n+n2-1,i+n-1, 1)) }
    
    else {links.add<-rbind( c(n+n2-1,i+n-1, 1), c(n+n1-1,i+n-1, 1))}
    
    links<-rbind(links, links.add)
    
  }
  
  names(links)<-c("source", "target", "value")
  
  new.nodes<-paste("node ", (1:max(m))+n)
  
  nodes<-data.frame(name=c(hc$labels, new.nodes), group=c(rep(1, max(m)), rep(2, n)))
  
  return(list(links=links, nodes=nodes))
  
}


#Load packages for convertinng to JSON
library(rjson)
library(stringr)

#Function for converting to JSON
dfToJSON<-function(df, mode='vector'){
  
  colToList<-function(x, y){
    
    col.json<-list()
    
    #Build up a list of coordinates
    
    for (i in 1:length(x)){
      
      ni<-list(x=x[i], y=y[i])
      col.json[[length(col.json)+1]]<-ni
    }
    
    return(col.json)
    
  }
  
  
  if (mode=='vector'){
    
    for.json<-list()
    
    for (j in 1:ncol(df)){
      for.json[[length(for.json)+1]]<-list(name=colnames(df)[j] , data=df[,j])
    }
    
  }
  
  if (mode=='coords') {
    
    for.json<-list()
    
    for (j in 2:ncol(df)){
      for.json[[length(for.json)+1]]<-list(name=colnames(df)[j] , data=colToList(x=df[,1], y=df[,j]))
    }
    
  }
  
  if (mode=='rowToObject') {
    
    for.json<-list()
    
    for (j in 1:nrow(df)){
      # for.json[[length(for.json)+1]]<-list(df[j,])
      for.json[[length(for.json)+1]]<-df[j,]
    }
    
  }
  
  jj<-toJSON(for.json)
  
  return(jj)
  
}

eg<-extractGraph(hc) 
e<-dfToJSON(eg$links,  'rowToObject')
n<-dfToJSON(eg$nodes,  'rowToObject')

fileConn<-file("/path/hcGraph.jsonp")
writeLines(paste0("graphIG={ \"nodes\":", n, ", \"links\": ", e, "}"), fileConn)
close(fileConn)

Thanks a lot