jamesthomson/HClust_Dendogram.R

## HClust_Dendogram.R
library(rjson)

#convert output from hclust into a nested JSON file

HCtoJSON<-function(hc){

  labels<-hc$labels
  merge<-data.frame(hc$merge)

  for (i in (1:nrow(merge))) {

    if (merge[i,1]<0 & merge[i,2]<0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(list(name=labels[-merge[i,1]]),list(name=labels[-merge[i,2]])))")))}
    else if (merge[i,1]>0 & merge[i,2]<0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(node", merge[i,1], ", list(name=labels[-merge[i,2]])))")))}
    else if (merge[i,1]<0 & merge[i,2]>0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(list(name=labels[-merge[i,1]]), node", merge[i,2],"))")))}
    else if (merge[i,1]>0 & merge[i,2]>0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(node",merge[i,1] , ", node" , merge[i,2]," ))")))}
  }

  eval(parse(text=paste0("JSON<-toJSON(node",nrow(merge), ")")))

  return(JSON)
}


#wrap nested JSON file into d3 html

D3Dendo<-function(JSON, text=15, height=800, width=700, file_out){

  header<-paste0("<!DOCTYPE html>
                 <meta charset=\"utf-8\">
                 <style>

                 .node circle {
                 fill: #fff;
                 stroke: steelblue;
                 stroke-width: 1.5px;
                 }

                 .node {
                 font: ",text , "px sans-serif;
                 }

                 .link {
                 fill: none;
                 stroke: #ccc;
                 stroke-width: 1.5px;
                 }

                 </style>
                 <body>
                 <script src=\"http://d3js.org/d3.v3.min.js\"></script>

                 <script type=\"application/json\" id=\"data\">")


  footer<-paste0("</script>


  <script>

  var data = document.getElementById('data').innerHTML;
  root = JSON.parse(data);


  var width = ", width, ",
  height = ", height, ";

  var cluster = d3.layout.cluster()
  .size([height-50, width - 160]);

  var diagonal = d3.svg.diagonal()
  .projection(function(d) { return [d.y, d.x]; });

  var svg = d3.select(\"body\").append(\"svg\")
  .attr(\"width\", width)
  .attr(\"height\", height)
  .append(\"g\")
  .attr(\"transform\", \"translate(40,0)\");


  var nodes = cluster.nodes(root),
  links = cluster.links(nodes);

  var link = svg.selectAll(\".link\")
  .data(links)
  .enter().append(\"path\")
  .attr(\"class\", \"link\")
  .attr(\"d\", diagonal);

  var node = svg.selectAll(\".node\")
  .data(nodes)
  .enter().append(\"g\")
  .attr(\"class\", \"node\")
  .attr(\"transform\", function(d) { return \"translate(\" + d.y + \",\" + d.x + \")\"; })

  node.append(\"circle\")
  .attr(\"r\", 4.5);

  node.append(\"text\")
  .attr(\"dx\", function(d) { return d.children ? 8 : 8; })
  .attr(\"dy\", function(d) { return d.children ? 20 : 4; })
  .style(\"text-anchor\", function(d) { return d.children ? \"end\" : \"start\"; })
  .text(function(d) { return d.name; });


  d3.select(self.frameElement).style(\"height\", height + \"px\");

  </script>")

  fileConn<-file(file_out)
  writeLines(paste0(header, JSON, footer), fileConn)
  close(fileConn)

}


hc <- hclust(dist(USArrests), "ave")
plot(hc)
JSON<-HCtoJSON(hc)
D3Dendo(JSON, file_out="/Users/home/Documents/R_Projects/D3/USArrests_Dendo.html")
	library(rjson)

	#convert output from hclust into a nested JSON file

	HCtoJSON<-function(hc){

	labels<-hc$labels
	merge<-data.frame(hc$merge)

	for (i in (1:nrow(merge))) {

	if (merge[i,1]<0 & merge[i,2]<0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(list(name=labels[-merge[i,1]]),list(name=labels[-merge[i,2]])))")))}
	else if (merge[i,1]>0 & merge[i,2]<0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(node", merge[i,1], ", list(name=labels[-merge[i,2]])))")))}
	else if (merge[i,1]<0 & merge[i,2]>0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(list(name=labels[-merge[i,1]]), node", merge[i,2],"))")))}
	else if (merge[i,1]>0 & merge[i,2]>0) {eval(parse(text=paste0("node", i, "<-list(name=\"node", i, "\", children=list(node",merge[i,1] , ", node" , merge[i,2]," ))")))}
	}

	eval(parse(text=paste0("JSON<-toJSON(node",nrow(merge), ")")))

	return(JSON)
	}


	#wrap nested JSON file into d3 html

	D3Dendo<-function(JSON, text=15, height=800, width=700, file_out){

	header<-paste0("<!DOCTYPE html>
	<meta charset=\"utf-8\">
	<style>

	.node circle {
	fill: #fff;
	stroke: steelblue;
	stroke-width: 1.5px;
	}

	.node {
	font: ",text , "px sans-serif;
	}

	.link {
	fill: none;
	stroke: #ccc;
	stroke-width: 1.5px;
	}

	</style>
	<body>
	<script src=\"http://d3js.org/d3.v3.min.js\"></script>

	<script type=\"application/json\" id=\"data\">")


	footer<-paste0("</script>




	<script>

	var data = document.getElementById('data').innerHTML;
	root = JSON.parse(data);


	var width = ", width, ",
	height = ", height, ";

	var cluster = d3.layout.cluster()
	.size([height-50, width - 160]);

	var diagonal = d3.svg.diagonal()
	.projection(function(d) { return [d.y, d.x]; });

	var svg = d3.select(\"body\").append(\"svg\")
	.attr(\"width\", width)
	.attr(\"height\", height)
	.append(\"g\")
	.attr(\"transform\", \"translate(40,0)\");


	var nodes = cluster.nodes(root),
	links = cluster.links(nodes);

	var link = svg.selectAll(\".link\")
	.data(links)
	.enter().append(\"path\")
	.attr(\"class\", \"link\")
	.attr(\"d\", diagonal);

	var node = svg.selectAll(\".node\")
	.data(nodes)
	.enter().append(\"g\")
	.attr(\"class\", \"node\")
	.attr(\"transform\", function(d) { return \"translate(\" + d.y + \",\" + d.x + \")\"; })

	node.append(\"circle\")
	.attr(\"r\", 4.5);

	node.append(\"text\")
	.attr(\"dx\", function(d) { return d.children ? 8 : 8; })
	.attr(\"dy\", function(d) { return d.children ? 20 : 4; })
	.style(\"text-anchor\", function(d) { return d.children ? \"end\" : \"start\"; })
	.text(function(d) { return d.name; });


	d3.select(self.frameElement).style(\"height\", height + \"px\");

	</script>")

	fileConn<-file(file_out)
	writeLines(paste0(header, JSON, footer), fileConn)
	close(fileConn)

	}



	hc <- hclust(dist(USArrests), "ave")
	plot(hc)
	JSON<-HCtoJSON(hc)
	D3Dendo(JSON, file_out="/Users/home/Documents/R_Projects/D3/USArrests_Dendo.html")