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What does your data structure look like? Can you please upload a Tableau Packaged Workbook with so sample data to support your scenario?
I'd imagine you could write a calculated field to force one set of data to be negative and drop that on the color shelf so it wouldn't impact the actual data. For example;
SUM(IF Region = 'Central' or [Region] = 'South' then [Profit]*-1
Brilliant, thank you. I'm clearly trying to overcomplicate things!