CLR transformation plots/model


I am using the following code to test if PN (a continuous variable) is associated with the clr-abundance of my pathways

However, the generated output scatter plots all have CPM values on the y-axis and not the clr transformed values that would be used for modeling. Is there a way to change the y-axis of the plots?

DA_PN_clr = Maaslin2( input_data = DA_pathway,
input_metadata = DA_meta,
min_abundance = 0.00001,
min_prevalence = 0.1,
normalization = “CLR”,
transform = “NONE”,
output = “PN_output_clr”,
fixed_effects = c(“PN”),
random_effects = c(“Subject”),
standardize = FALSE,
min_variance = 0.0,
reference = NULL,
max_significance = 0.25,
analysis_method = “LM”,
correction = “BH”)

hi @tappituffi2 ,

Maaslin2 doesn’t currently have a feature that would allow you to change the y-axis to CLR normalization. We are looking into updating this in the future.