Thanks for a good tool.

I have four factors in a predictive variable; Q1, Q2, Q3, and Q4.

I’ve set Q1 as a reference.

However, I found that the order of the x-axis labels was Q1, Q3, Q2, and Q4 in scatter plots.

I tried to change the labels of the variable with A, B, C, and D, but the trouble was the same such as A, C, B, and D orders.

I think this problem happened after updating with a new version of Maaslin2 including the reference option.

Could you check this problem?

The version of Maaslin2 I used is 1.8.0 in R.

I also faced the same problem. Really happy if any can help,

Thank you.

Hi @Han-Na_Kim,

I’m not sure what is happening here, MaAsLin should default to base R for things like order, and R would have ordered these 1. by increasing order and 2. alphabetically. I don’t think this is a MaAsLin issue per say, can you check your metadata object by running the `str()`

command? Is there some inherent ordering on that level?

If nothing else you can always force an order `meta$cat = factor(meta$cat, levels = c("A", "B", "C", "D"))`

. The current version of MaAsLin may ignore this attempt. In which case, you can always pull out the data and use `ggplot`

to plot the data. We are working on outputting the ggplot objects for a future version of MaAsLin but in the meantime it is pretty easy to do that outside of the library.

I hope this helps,

Kelsey

Thanks for your reply.

I’ve already tried to force the order such as factor(data$variable, levels=c(“Q1”,“Q2”,“Q3”,“Q4”)), but same problem is happenned.

When I run the str(variable), it showed $variable: Factor w/4 levels “Q1”,“Q2”,“Q3”,…:1 1 1 1 1 1 …