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Alright, I gave it a go. Like I said, a flowchart-type view makes a ton of sense to me. You can just follow two dotted lines and end up with all the possible combinations. For a male-cat, the Y-chromosone in the middle prevents that you are able to select both black & orange.
Also, some other considerations:
– The gender is important for the mating, so I gave it a color and different position to differentiate more. But I also think it can be more of a background-feature, since your attention should be drawn to the genes more. So cropping the (well-known) icon is no problem I think, and might give your grid a more ‘designed’ feel.
– The ‘white’ spots genes will have a very light color. This is important – it should be very clear that the checkboxes are the only things that can be ‘filled in’. Leaving the gene-color white might confuse players if that’s a square you can fill in as well.
– Oh yeah, I think making the genes a more specific shape (diamonds seem good) also helps prevent confusion. People are used to color in circles & boxes.
– One extra variant for a lady-cat: to have the actual fur behind the checkbox to make it clearer what the genes actually do.