I am in a mission of finding the perfect whole wheat to plain flour ratio (because I had a HUGE disaster from the 100% wheat recipe.  So I had find a way to correct that recipe)  
 
pizza & cheesy flat bread — 2 cups of flour (75% whole wheat, 25% AP)
tiny puffy wheat square bread — 300g ( 60% whole wheat, 40% AP)
regular bread machine loaf — 3 cups of flour (50% whole wheat, 50%)
 
75% wheat resulted in  a bit firmer and chewy for pizza which is great.  It has an wonderful nutty taste.  The tiny wheat squares are very cute and extremely easy to shape.  Just roll out the dough flat and fold a few times.  When you can form a 8" x 8" square (not need to be perfect square), then cut into 9 even squares.  Baking in 350F oven for 12 mins.
 
I don’t think there is a fix ratio.  It really depends on the kind of bread/dough you make and adjust the ratio accordingly.  I will definitely remain using high whole wheat ration for pizza crust because it turned out soo good!
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