Reference factor present in Maaslin2 heatmap


I am using Maaslin2 to find assocation between taxa with a few metadata, I set age, gender, BCcat as fixed_effects. Under BCcat there are three categories (NC, PN and UC), I set reference = “BCcat, NC”.

So it means compare PN and UC with reference to NC.
However, BCcat NC is present in my heatmap. Can anyone enlighten me why is it so? I thought BCcat PN and BCcat UC should be on the heatmap instead if there is any significant association?

Thank you in advance!

Hi @SC07,

You are correct if MaAsLin is seeing something as the reference it shouldn’t be in the heatmap. I think the issue might be in your setting of the reference level have you tried reference = c(“BCcat,NC”)? I think that might fix it - but let us know if it doesn’t!