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I'm not completely sure, but is it maybe the property rapidminer.gui.plotter.matrixplot.size under Tools/Properties/Gui?
Are you sure that "category" refers to the product of bars and stack levels? I would rather think that it refers to the number of bars and/or the number of levels.
Maybe you can configure the plot differently or apply a different preprocessing on your data?
You can also try to use the Advanced Charts to create stacked bar charts in a more flexible way than with the usual Plot View.
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