Generates the data for comparing two clusters using a Sankey diagram

SankeyClusComp

clusComp<-function(cl1, cl2, num.clus){

#Set up object for recording clusters
clus.change<-NULL

ct1<-cutree(cl1, k=num.clus)
add.1<-data.frame(size=rep(1, length(ct1)), ind=names(ct1), cluster=paste0(1, ".", ct1))
ct2<-cutree(cl2, k=num.clus)
add.2<-data.frame(size=rep(2, length(ct2)), ind=names(ct2), cluster=paste0(2, ".", ct2))

clus.change<-rbind(add.1, add.2)

#Reshape the data
m<-merge(clus.change, clus.change, by="ind")
d<-dcast(data=m, size.x+size.y+cluster.x+cluster.y~., length)

#Filter to just the sequential steps

ex<-d[d$size.y==(d$size.x+1),3:5]

#Create the nodes

ind.list<-ddply(.data=clus.change[,c(3,2)], .(cluster), .fun= function(x) paste0(x[,2], collapse=" <br> "))
nodes.df<-ind.list
names(nodes.df)<-c("name", "ind")

#Convert 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)
  
}

n<-dfToJSON(nodes.df,  'rowToObject')

#Create the edges

links<-NULL
for (i in 1:nrow(ex )){
  
  s<-which(nodes.df$name==ex$cluster.x[i])-1
  t<-which(nodes.df$name==ex$cluster.y[i])-1
  links<-rbind(links, data.frame(source=s,target=t, value=ex[i,3]))
}

e<-dfToJSON(links,  'rowToObject')

graph<-list(nodes=n, edges=e)

return(graph)

}


library(rjson)
library(stringr)
library(reshape2)

cc<-clusComp(cl1, cl2, 80)

fileConn<-file("path/sankeyClustersTest.jsonp")
writeLines(paste0("{ \"nodes\":", cc$nodes, ", \"links\": ", cc$edges, "}"), fileConn)
close(fileConn)