Price Difference: Copper Vs. Pex

I'm having an empty upstairs room converted to a bathroom.
The contract has a plumbing line item, $3900. Separate from fixtures. The contract specifies all copper for the supply lines. Without telling me, they installed the plastic stuff instead.
I realize it's hard to talk specific pricing without seeing the job, but:
How much should they knock off for not using copper? They said on the phone "you'll get a credit, there's a big difference in the material and labor."
There are six fixtures to feed with the supply lines - a five drop bathroom. There was no plumbing upstairs before this. It's a big bathroom, about 9x18.
If anyone could give me a percentage difference for installing one versus the other, even that would help. I'm just looking for information to give me an informed view of this.

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