r2d3.r

#To Create a "bundle" of topics in D3 as created by Bostock- https://github.com/mbostock/d3/wiki/Bundle-Layout
#First  we need to go from R hcluster to JSON for the d3.
#This is mostly derived from Rolf Fredheim's frametoD3.r function at https://github.com/fredheir/frameToD3

#Load Libraries
#install.packages("data.table")
require(data.table)
#install.packages("RJSONIO")
require(RJSONIO)

#Hierarchival cluster
hc <- hclust(dist(topic.words), method= "ward.D")
plot(hc, labels = topics.labels)

#now we split the data based on membership structure. We will take four levels:
#(basically this means we will calculate which group each variable belongs in for different levels of the tree strucutre)
memb2 <- as.character(cutree(hc, k = 2))
memb6 <- as.character(cutree(hc, k = 6))
memb15 <- as.character(cutree(hc, k = 15))
memb40 <- as.character(cutree(hc, k = 40))

#Now put this information into a table, together with the labels and the order in which they should appear:
b=data.table(memb2,memb6,memb15,memb40, label=topics.labels, order=hc$order)

#sort the data so it alligns with the structure calculated using hclust()
setkey(b,order)
#drop the order variable:
b[,order:=NULL]

#we define a function which will create a nested list in JSON format:
#From here: http://stackoverflow.com/questions/12818864/how-to-write-to-json-with-children-from-r
makeList<-function(x){
  if(ncol(x)>2){
    listSplit<-split(x[-1],x[1],drop=T)
    lapply(names(listSplit),function(y){list(name=y,imports=makeList(listSplit[[y]]))})
  }else{
    lapply(seq(nrow(x[1])),function(y){list(name=x[,1][y],size=x[,2][y])})
  }
}


#This will not work on a data.table

b <- data.frame(b)
out <- makeList(b)
#Have a look at the structure this creates:
print (head(out))


#Basically we have made a list of lists containing the information from the tree diagram.
#Finally we put everythin into a list, convert this to json format and save it as data.json
jsonOut<-toJSON(list(name="Centre",children=makeList(b)))

#We use the cat function here, because in some cases you may want to add separators, or a prefix and suffix to make the formatting just right
cat(jsonOut,file="topics.json")