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If you could be more explicit in exactly what is/is not being scaled, that could be helpful. Since you are using Matlab graphics, I am not sure how they are being converted to Sage. But maybe this will be helpful.

A Sage-generated graphic can be controlled using the figsize option. Compare the following commands' outputs.

sage: plot(sin(x),(x,-pi,pi),figsize=[2,3])

sage: plot(sin(x),(x,-pi,pi),figsize=[1,6])

sage: plot(sin(x),(x,-pi,pi),aspect_ratio=1)

sage: plot(sin(x),(x,-pi,pi),aspect_ratio=1,figsize=[3,4])

Incidentally, Ticket 2100 has some good updates to this. We are just waiting on some final minor review for that.