Here is an example of the pack layout in d3js:
http://bl.ocks.org/4063530
Is it possible to control the colors of the individual cirles?
Here is another example of the pack layout with colors:
http://bl.ocks.org/4063269

Can you help me understand how the colors are assigned to the bubbles in the second chart?
You can just add the attribute fill to change the color:
node.append("circle")
.attr("r", function(d) { return d.r; })
.style("fill", function(d){ return d.color; });
In the example above, suppose your data contains a color field.
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