Reference levels Milo pertpy

Ecosystem pertpy
1

Hi @Zethson ,

I am struggling a bit with specifying contrasts for Milo in Pertpy.
I have a column diagnosis with levels ICM_AMI, control,DCM,ICM_AMI
I want to do a lot of comparisons so I do this:

design = "~ Donor_Sex + Sample_Prep  + diagnosis"

contrasts = [
    "diagnosisICM_AMI - diagnosiscontrol",
    "diagnosisDCM - diagnosiscontrol",
    "diagnosisICM - diagnosiscontrol",
    "diagnosisICM - diagnosisDCM",
    "diagnosisICM_AMI - diagnosisICM",
]

for contrast in contrasts:
    print(contrast)
    milo.da_nhoods(mdata, design=design, model_contrasts=contrast)
    mdata["milo"].var.to_csv(contrast.replace(" ", "_") + ".csv")

But as soon as a contrast with diagnosisDCM is encountered it crashes because the object cannot be found.
I think this might be because it got chosen as reference level?
If I load everything into R

# control is reference level here
mod_contrast <- makeContrasts(
    DCM_vs_Control = diagnosisDCM,
    levels = model_mat_cols
)

works.
How do I specify this correctly on the Python side?

Thanks a lot!