When creating your comparative analysis, you have the option to assign specific colors and order to the metadata variables of interest. In the Create CA page (after you’ve split samples into cohorts), you can drag-and-drop cohorts around to match your desired order. You can also change the colors using the color switcher. These will be reflected in the generated comparative analysis.Documentation Index
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Comparative Analysis and Statistics
Changing Order and Color of Cohorts in CA Visualizations
Customize the color and order of cohorts/metadata groups when generating a comparative analysis.