d3 bar chart axis alignment - d3.js

Question

I am trying to use the margin conventions described in http://bl.ocks.org/mbostock/3019563
when plotting bar charts. However, the bars do not align with the x-axis as you can see
in this basic example: http://bl.ocks.org/kyrre/bbd29f225173825797e3. What am I doing wrong?
var data = [
{x: "Differential Geometry", y: 10},
{x: "Statistical Physics", y: 5},
{x: "Music", y: 3}
]
var margin = {top: 20, right: 10, bottom: 20, left: 50};
var width = 500 - margin.left - margin.right;
var height = 320 - margin.top - margin.bottom;
var y = d3.scale.linear()
.domain([0, d3.max(data, function(x) {
return x.y;
})])
.range([0, height]);
var x = d3.scale.ordinal()
.domain(_.map(data, function(d) { return d.x;}))
.rangeRoundBands([0, width], 0.10);
var xAxis = d3.svg.axis()
.scale(x)
.orient("bottom");
var yAxis = d3.svg.axis()
.scale(y)
.orient("left");
var svg = d3.select("body")
.append("svg")
.attr("width", width + margin.left + margin.right)
.attr("height", height + margin.top + margin.bottom)
.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
var rect = svg.selectAll("rect")
.data(data)
.enter()
.append("rect")
.attr("x", function(d) {
return x(d.x);
})
.attr("y", 0)
.attr("height", function(d) {
return y(d.y);
})
.attr("fill", function(d) { return "blue";})
.attr("width", 20);
svg.append("g")
.attr("class", "x axis")
.attr("transform", "translate(0," + height + ")")
.call(xAxis);
svg.append("g")
.attr("class", "y axis")
.attr("transform", "translate(0,0)")
.call(yAxis);

Answer 1

The y coordinates are counted from the top (i.e. 0 is at the top of the image). It should work if you set y to the total minus height.
.attr("y", function(d) { return (height - y(d.y)); })