BayraktarLab / cell2location

Comprehensive mapping of tissue cell architecture via integrated single cell and spatial transcriptomics (cell2location model)
https://cell2location.readthedocs.io/en/latest/
Apache License 2.0
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How do I find where run_colocation stores its results in adata? #368

Open singhbhavya opened 5 months ago

singhbhavya commented 5 months ago

Please use the template below to post a question to https://discourse.scverse.org/c/ecosytem/cell2location/.

Problem

Hi there! I followed the tutorial for "Identifying cellular compartments / tissue zones using matrix factorisation (NMF)". I successfully ran run_colocation, and all the results files were created. I am just confused about where the resulting data is stored in the adata itself. According to the tutorial, it should be in adata.uns[f"mod_coloc_n_fact{n_fact}"], but I haven't been able to obtain them for any of the factor numbers - every time, I get a key error when I do adata.uns["mod_coloc_n_fact10"].