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vandijklab / CINEMA-OT

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Ref_label and expr_label in notebook tutorial switched #11

Open ArturDev42 opened 5 months ago

ArturDev42 commented 5 months ago

Thanks for this interesting method! Incinemaot_tutorial.ipynb I noticed that the ref_label is set to the treatment IFNb. 

cf, ot, de = co.cinemaot.cinemaot_unweighted(
    adata_,
    obs_label="perturbation",
    ref_label="IFNb",
    expr_label="No stimulation",
    mode="parametric",
    thres=0.5,
    smoothness=1e-5,
    eps=1e-3,
    preweight_label="cell_type0528",
)

From the source code cinemaot.py I understand that the ref_label indicates the control group.

ref_label: 'str'
        A string for indicating the control group in adata.obs.values.

I assume that in the example above it should be ref_label="No stimulation" and expr_label="IFNb", correct? Thanks!

MingzeDong commented 1 day ago

Thanks for bringing this up! This problem arises from our early experiments when we switched "treatment effect on control cells" to "treatment effect on perturbed cells". This is fixed in the newer Pertpy implementation: https://github.com/scverse/pertpy .