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For exemple, is it possible to list all the possible diseases or cell types that can be used in the obs_value_filter ? Ideally in python ?
The text was updated successfully, but these errors were encountered:
@HugoCornu we can put up a sample notebook -- for the moment though here's a snippet. The gist is, read as Pandas and use .groupby().
.groupby()
def count_obs(exp: tiledbsoma.Experiment, attr_name: str) -> None: print( exp.obs.read(column_names=[attr_name]) .concat() .to_pandas() .groupby(attr_name) .size() .sort_values() )
>>> exp = tiledbsoma.Experiment.open(your_uri)
>>> exp.obs.schema soma_joinid: int64 not null obs_id: large_string not null ... cell_type: large_string not null ...
>>> count_obs(exp, 'cell_type') cell_type enteroendocrine cell of small intestine 18 paneth cell of epithelium of small intestine 34 transit amplifying cell of small intestine 53 smooth muscle fiber of ileum 54 mast cell 92 endothelial cell of lymphatic vessel 96 pericyte cell 121 glial cell 175 ileal goblet cell 230 progenitor cell 382 endothelial cell 565 fibroblast 571 enterocyte of epithelium proper of ileum 809 innate lymphoid cell 1382 mononuclear phagocyte 1635 B cell 3183 plasma cell 3898 native cell 4203 alpha-beta T cell 14957 dtype: int64
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johnkerl
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For exemple, is it possible to list all the possible diseases or cell types that can be used in the obs_value_filter ? Ideally in python ?
The text was updated successfully, but these errors were encountered: