I am using the D3 tree layout, such as this one: http://mbostock.github.com/d3/talk/20111018/tree.html
I have modified it for my needs and am running into an issue.
I know I'm not supposed to respond to other answers, but I don't have enough reputation to add a comment.
Anyway, I just wanted to update this for people using the latest d3.v3.js file. (I assume this is because of a new version, because the line references in the accepted answer were wrong for me.)
The d3.layout.tree function that you are editing is found between lines 6236 and 6345. d3_layout_treeVisitAfter starts on line 6318. The hierarchy variable is declared on line 6237. The bit about tree.elementsize still stands - I put it on line 6343.
Lastly (I assume this was an error): when you create the tree, put the dimensions inside square brackets, like you normally do with "size". So:
var tree = d3.layout.tree()
.size(null)
.elementsize([50, 240]);