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aertslab / pycisTopic

pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.
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run_umap error #160

Open strawberry098 opened 1 month ago

strawberry098 commented 1 month ago

I'm getting the following error for run_umap

image

where Cell is the column name containing cell ID values.

How can I resolve this?

SeppeDeWinter commented 1 month ago

Hi @strawberry098

Can you show the output of


print(cistopic_obj1_models)

print(cistopic_obj.selected_model)

All the best,

Seppe

strawberry098 commented 3 weeks ago

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 commented 3 weeks ago

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