Don't know if it helps, but I posted a sample script that takes an x,y coordinate list and creates a shape map from it:
https://community.jmp.com/t5/JMP-Scripts/Wafer-maps-in-Graph-Builder-using-Map-Shapes/ta-p/753839
It's intended to create semiconductor wafer maps and it's for demonstration purposes only so it's very simple - each x,y location is a square of unit size, which may not match your needs, but hopefully it shows a simple use case.
In general though the custom map generator add-in mentioned by @hogi will be much more powerful.