qiime emperor biplot with custom-axis

I would like to generate an emperor biplot to be able to view which taxa are driving the variation in my emperor plot and I tried using “–p-custom-axis” so that I could select “experiment day” as my third axis, like I did for my normal emperor plot but I got an error message that shows that there is no such command available for the emperor biplot? That seemed odd to me. Is that correct?

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@Lisa_Crummett, that is correct. We currently don’t support biplots with custom axes. The reason behind this is that arrow positions are dependent on the coordinates where they are projected. If you wanted to show arrows on a “custom axes” ordination, you would need to do the “custom axes” transform before projection, and there really isn’t any math/research benchmarking this approach.


Thank you for your quick reply Yoshiki.