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Error while loading custom data in NCEM #108
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Hi @archanabhardwaj, thank you for your interest in running ncem on your own data. Please store |
I am closing the issue for now, but feel free to open it again in case of further questions. |
Hello
I am trying to run NCEM after running the deconvolution in cell2location method. I followed entire workflow as given in https://github.com/theislab/ncem_benchmarks/blob/main/notebooks/data_preparation/deconvolution/cell2location_human_lymphnode.ipynb and saved dataset as "cell2location_test.h5ad" based on the information given in the "Collect ncem anndata object" section. Next, I tried to read h5ad data into NCEM for further analysis with custom loader function.
adata_vis # stores information of my cell2location_test.h5ad file
ncem = InterpreterInteraction()
ncem.data = customLoader(
adata=adata_vis, cluster='cell_type', patient='A1', library_id='sam_A1', radius=52
)
But its giving me error such as AttributeError: 'numpy.ndarray' object has no attribute 'toarray'
If I am doing something wrong, please correct me.
Thanks in advance
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