r - rCharts グラフを slidify スライド デッキに埋め込む

Question

rCharts を使用して作成したグラフを、スライド スライド デッキに取得しようとしています。rCharts が生成するスクリプトを slidify の .Rmd ファイルにコピーしようとしましたが、得られるのは空のスライドだけです。

.Rmd ファイルは次のとおりです。

---
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>

RI で .Rmd ファイルをコンパイルすると、次の出力が得られます。

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"

私がここで間違っていることについて何か考えはありますか? どうもありがとうございました！