Working with bar graphs, pie graphs, etc.

I'm working with somone who likes to create pie graphs, bar graphs and other charts. This guy is not a designer and is using Microsoft applications like Excel and PowerPoint to create these charts. My job is to bring these charts over to an ID document I'm working on. The black and white ones are no problem: I can convert them to a PDF, open them up in Photshop, and rasterize them. The color ones are screwed up. We are printing only black and one spot color, and Excel is apparently programmed to save color charts as RGB or CMYK. So my basic question is: what do you do for graphs? Is there a good application for making graphs that are design quality that knows how to do spot color? Or is it best to lay out graphs manually ID, by drawing lines, shapes and bars and coloring in the spot colors myself? Thanks.

Illustrator.
You should be able to bring your Excel or PowerPoint graphs into Illustrator as easily as into Photoshop.

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