Embedding rCharts graph into slidify slide deck - r

Question

I am still trying to get a graph that I have produced using rCharts into a slidify slide deck. I have tried copying the script that rCharts produces into slidify's .Rmd file but all I get is an empty slide.
Here is the .Rmd file:
---
title : Test Sankey
subtitle :
author : Matthew
job :
framework : io2012 # {io2012, html5slides, shower, dzslides, ...}
highlighter : highlight.js # {highlight.js, prettify, highlight}
hitheme : tomorrow #
widgets : [d3_sankey] # {mathjax, quiz, bootstrap}
mode : selfcontained # {standalone, draft}
---
Slide 1
---
The graph should be on the next slide.
---
<div id='sankey1' class='rChart d3_sankey'></div>
<script>
(function(){
var params = {
"dom": "sankey1",
"width": 960,
"height": 500,
"data": {
"source": [ "a", "b", "c", "d", "e", "a", "d", "f", "e", "g", "h", "j", "j", "k", "l", "q" ],
"target": [ "j", "d", "a", "q", "f", "k", "e", "g", "j", "e", "l", "c", "h", "b", "d", "a" ],
"value": [ 8, 1, 4, 6, 2, 1, 1, 1, 6, 9, 2, 2, 4, 6, 9, 1 ]
},
"nodeWidth": 15,
"nodePadding": 10,
"layout": 32,
"id": "sankey1"
};
params.units ? units = " " + params.units : units = "";
//hard code these now but eventually make available
var formatNumber = d3.format("0,.0f"), // zero decimal places
format = function(d) { return formatNumber(d) + units; },
color = d3.scale.category20();
if(params.labelFormat){
formatNumber = d3.format(".2%");
}
var svg = d3.select('#' + params.id).append("svg")
.attr("width", params.width)
.attr("height", params.height);
var sankey = d3.sankey()
.nodeWidth(params.nodeWidth)
.nodePadding(params.nodePadding)
.layout(params.layout)
.size([params.width,params.height]);
var path = sankey.link();
var data = params.data,
links = [],
nodes = [];
//get all source and target into nodes
//will reduce to unique in the next step
//also get links in object form
data.source.forEach(function (d, i) {
nodes.push({ "name": data.source[i] });
nodes.push({ "name": data.target[i] });
links.push({ "source": data.source[i], "target": data.target[i], "value": +data.value[i] });
});
//now get nodes based on links data
//thanks Mike Bostock https://groups.google.com/d/msg/d3-js/pl297cFtIQk/Eso4q_eBu1IJ
//this handy little function returns only the distinct / unique nodes
nodes = d3.keys(d3.nest()
.key(function (d) { return d.name; })
.map(nodes));
//it appears d3 with force layout wants a numeric source and target
//so loop through each link replacing the text with its index from node
links.forEach(function (d, i) {
links[i].source = nodes.indexOf(links[i].source);
links[i].target = nodes.indexOf(links[i].target);
});
//now loop through each nodes to make nodes an array of objects rather than an array of strings
nodes.forEach(function (d, i) {
nodes[i] = { "name": d };
});
sankey
.nodes(nodes)
.links(links)
.layout(params.layout);
var link = svg.append("g").selectAll(".link")
.data(links)
.enter().append("path")
.attr("class", "link")
.attr("d", path)
.style("stroke-width", function (d) { return Math.max(1, d.dy); })
.sort(function (a, b) { return b.dy - a.dy; });
link.append("title")
.text(function (d) { return d.source.name + " → " + d.target.name + "\n" + format(d.value); });
var node = svg.append("g").selectAll(".node")
.data(nodes)
.enter().append("g")
.attr("class", "node")
.attr("transform", function (d) { return "translate(" + d.x + "," + d.y + ")"; })
.call(d3.behavior.drag()
.origin(function (d) { return d; })
.on("dragstart", function () { this.parentNode.appendChild(this); })
.on("drag", dragmove));
node.append("rect")
.attr("height", function (d) { return d.dy; })
.attr("width", sankey.nodeWidth())
.style("fill", function (d) { return d.color = color(d.name.replace(/ .*/, "")); })
.style("stroke", function (d) { return d3.rgb(d.color).darker(2); })
.append("title")
.text(function (d) { return d.name + "\n" + format(d.value); });
node.append("text")
.attr("x", -6)
.attr("y", function (d) { return d.dy / 2; })
.attr("dy", ".35em")
.attr("text-anchor", "end")
.attr("transform", null)
.text(function (d) { return d.name; })
.filter(function (d) { return d.x < params.width / 2; })
.attr("x", 6 + sankey.nodeWidth())
.attr("text-anchor", "start");
// the function for moving the nodes
function dragmove(d) {
d3.select(this).attr("transform",
"translate(" + (
d.x = Math.max(0, Math.min(params.width - d.dx, d3.event.x))
) + "," + (
d.y = Math.max(0, Math.min(params.height - d.dy, d3.event.y))
) + ")");
sankey.relayout();
link.attr("d", path);
}
})();
</script>
When I compile the .Rmd file in R I get the following output:
slidify("index.Rmd")
processing file: index.Rmd
|.................................................................| 100%
ordinary text without R code
output file: index.md
Copying files to libraries/frameworks/io2012...
Copying files to libraries/highlighters/highlight.js...
Copying files to libraries/widgets/d3_sankey...
[1] "index.html"
Any idea on what I am doing wrong here? Thank you very much!