Hi Aleks,
You can just treat m as any symoblic expression and call it as a function.
sage: x,y = var('x,y')
sage: m = matrix([[cos(x),0],[0,-sin(y)]])
sage: m
[ cos(x) 0]
[ 0 -sin(y)]
sage: m(x=1, y=2)
[ cos(1) 0]
[ 0 -sin(2)]
sage: m.variables()
(x, y)
sage: m(1,2)
[ cos(1) 0]
[ 0 -sin(2)]
--Mike
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