I like to start by determining the simplest way to communicate the data I’ve been given. Things get complicated very quickly, so there’s no use in starting with an intricate base visualization if it needs to have numerous labels or additional dimensions of data applied.
I will use Illustrator or Processing (for more complex data) to create an initial rendering of the information. With Processing, I’ve developed an arsenal of graphing tools that will quickly allow me see the shape of the data I’m working with. I can then take the pdf output and style it with either Adobe Illustrator or InDesign.