D3 tree square node not in desired position - d3.js

Question

I want to create a tree view using d3 like this one http://bl.ocks.org/mbostock/4339083,
but instead of circles in node, I would like to have squares. I found this post that gave me a clue d3.js: modifyng links in a tree layout but not solved my issue. This is my fiddle http://jsfiddle.net/yp7o8wbm/ .
As you can see, all node are not in the correct position.
This is the js code:
var margin = {top: 20, right: 120, bottom: 20, left: 120},
width = 960 - margin.right - margin.left,
height = 500 - margin.top - margin.bottom;
var rectSize = 40;
var i = 0;
var tree = d3.layout.tree().size([height, width]);
var diagonal = d3.svg.diagonal()
.source(function(d) { return {"x":d.source.x, "y":(d.source.y+rectSize)}; })
.target(function(d) { return {"x":(d.target.x), "y":d.target.y}; })
.projection(function(d) { return [d.y, d.x]; });
var svg = d3.select("body").append("svg")
.attr("width", width + margin.right + margin.left)
.attr("height", height + margin.top + margin.bottom)
.append("g")
.attr("transform", "translate(" + margin.left + "," + margin.top + ")");
root = treeData[0];
update(root);
function update(source) {
// Compute the new tree layout.
var nodes = tree.nodes(root).reverse(),
links = tree.links(nodes);
// Normalize for fixed-depth.
nodes.forEach(function(d) { d.y = d.depth * 180; });
// Declare the nodes…
var node = svg.selectAll("g.node")
.data(nodes, function(d) { return d.id || (d.id = ++i); });
// Enter the nodes.
var nodeEnter = node.enter().append("g")
.attr("class", "node")
.attr("transform", function(d) {
return "translate(" + d.y + "," + d.x + ")"; });
nodeEnter.append("rect")
.attr("x", function(d) { return d.x ; })
.attr("y", function(d) { return d.y ; })
.attr("width", rectSize)
.attr("height", rectSize);
nodeEnter.append("text")
.attr("x", function(d) {
return d.children || d._children ? -13 : 13; })
.attr("dy", ".35em")
.attr("text-anchor", function(d) {
return d.children || d._children ? "end" : "start"; })
.text(function(d) { return d.name; })
.style("fill-opacity", 1);
// Declare the links…
var link = svg.selectAll("path.link")
.data(links, function(d) { return d.target.id; });
// Enter the links.
link.enter().insert("path", "g")
.attr("class", "link")
.attr("d", diagonal);
}
I can not realize where is the error in my code?

Answer 1

You are setting the position twice in different ways:
var nodeEnter = node.enter().append("g")
.attr("class", "node")
.attr("transform", function(d) {
return "translate(" + d.y + "," + d.x + ")"; //<-- setting it on the parent using a "translate"
});
nodeEnter.append("rect")
.attr("x", function(d) { return d.x ; }) //<-- setting it on the rect using a "x" attribute
Do this instead:
nodeEnter.append("rect")
.attr("x", 0) //<-- x is taken care of by translate
.attr("y", -rectSize/2) //<-- just use y to center the rect
.attr("width", rectSize)
.attr("height", rectSize);
Updated fiddle.