pm.pp.compensate(adata) how to know it working?

[KunHHE]

Description of feature

Hi @mbuttner, thanks for this tool development. May I ask you so we finished spectra flow cytometry, and it is always necessary to check the compensation before moving forward to analysis. SO in this pipeline, pm.pp.compensate(adata) how to know it's working and if the potential compensation is corrected or adjusted? Is there any way to view the flow plots channel by channel like in the flowjo to see if there are spillovers? Thank you!

[mbuttner]

Hi @KunHHE
I am glad to hear that you find the tool useful! The one time that I worked with spectral flow cytometry, I checked the pairwise scatter plots of selected markers after compensation to see if there are any co-correlation structures visible. You can plot the individual markers by

sc.pl.scatter(adata, x='marker_1', y='marker_2', color= 'sample_id')

where marker_1, marker_2 and sample_id have to be in the var_names or features stored in .obs as columns.
Please let me know if that is the visualization you are looking for or if you where thinking of anything else.