What information is stored in adata.varm['tacco_key']

[RunyuXia]

Hi! I was wondering if you could help me understand how to interpret the information stored in adata.varm['tacco_key'] after running TACCO. What exactly does it represent?

Thanks so much!

[JWatter]

Hi, sorry for the late reply. TACCO writes the reference profiles into adata_reference.varm, in case they are not found there already. https://github.com/simonwm/tacco/blob/87252c6ffcf5f616ffbf167a8d4d34bb8d86d276/tacco/tools/_annotate.py#L734

Meaning, you can write reference profiles into this slot manually and TACCO will use them instead. The reference profiles are "idealized" representations of the cell types in the reference datasets. A particular reference profile is the average expression of all cells of that type in the reference data.

For a conceptual overview of how the reference profiles are used refer to the TACCO overview notebook https://simonwm.github.io/tacco/notebooks/overview.html or Figure 1. from the paper https://www.nature.com/articles/s41587-023-01657-3#Fig1.

Hope this helps!