I'm looking for a free scatter plot html5/javascript library that allows setting color & alpha for each point.
I know that http://www.rgraph.net/ has this functionality, but I'm looking for a library with a less restrictive license.
You can probably accomplish this using Raphael.js. Here's a sample scatter plot from their demo site: http://raphaeljs.com/github/dots.html
And you might consider using this as a jumping-off point: https://github.com/stringfellow/raphael-scatter