How to use coef_plot_vars?

Downstream analysis and statistics MaAsLin
1

We’d like to force Maaslin3 to plot our main categorical variables (experimental groups) as the coefficient plots (instead of them sometimes going to heatmap part). We tried to do this by the coef_plot_vars but apparently fail to format the variables properly, as this leads to the output missing the summary plot altogether.

The manual says: categorical variables should be of the form "[variable] [level]"
So how exactly should we format this, if our variable is “exp_group” and the levels to be plotted are P and T?

We tried like:
coef_plot_vars = ‘[exp_group] [P,T]’
and other possible formats but it didn’t work, so I guess we did it wrong anyway…

2

Probably the easiest way to do this is to look at the original plot, exactly copy the name from the heatmap column (where you don’t want it), and use maaslin_plot_from_output with the name in coef_plot_vars.