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Which factor level to compare with


I want to find the associations of taxons with disease status (two status, Non-critical/Critical). And at the same time, I also have healthy controls. I ran MaAsLin, and the result seems to be always compared to Critical status. But i want to compare among these three groups or both compared to Healthy controls? How should i prepare the input?

Hi @Qiuyu-dot - this is something we have recently added. If you install the latest development version from Github (, you will see that there is an option called reference which can be used to specify references for categorical variables.

Hi himel

continuing this question, even after reference level we would not be able to see all pairwise comparisons in one heat map correct?
For example, If I want to essentially do pairwise comparisons and also learn what taxa in B and C are different from each other, as I understand it, I would re-run the analysis with level B (or C) as the reference. Is this correct? But in this case I need to run 7 times same analysis to get all pairwise comparisons that I need to check! But I would like to see all comparisons in one heat map instead of several? Is this possible with Maaslin2?

Thanks a lot, Rogi

Hi @roghaieh_ashrafi - as replied in the other thread, once you get the appropriately adjusted p-values and q-values, you can use an external package like Complexheatmap or pheatmap to create a heatmap that includes all the individual comparisons in the same figure. Unfortunately, this is currently not possible with the default MaAsLin 2 workflow.

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