run_umap error

[strawberry098]

I'm getting the following error for run_umap

where Cell is the column name containing cell ID values.

How can I resolve this?

[SeppeDeWinter]

Hi @strawberry098

Can you show the output of

print(cistopic_obj1_models)

print(cistopic_obj.selected_model)

All the best,

Seppe

[strawberry098]

Hi @SeppeDeWinter

print(cistopic_obj1_models) CistopicObject from project cisTopic with n_cells × n_regions = 92054 × 201656

print(cistopic_obj1_models.selected_model) CistopicLDAModel with 40 topics and n_cells × n_regions = 92054 × 201656

Thank you

[SeppeDeWinter]

Hi @strawberry098

I see with the issue is now, you spelled "Cell" with a capital "C", it should be "cell". Now the function should raise an error when this occurs: https://github.com/aertslab/pycisTopic/commit/787ce422a37f5975b0ebb9e7b19eeaed44847501.

All the best,

Seppe