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improve options for low count filters and add data dashboard module #64

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May 23, 2024
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mend
abearab committed May 22, 2024
commit 26a2383a9ffd0a9fb0dc3efab53b6dfd4d107d63
2 changes: 1 addition & 1 deletion screenpro/utils.py
Original file line number Diff line number Diff line change
@@ -44,7 +44,7 @@ def find_low_counts(adata, filter_type='either', minimum_reads=50):
# print the number of removed variables
n_removed = adata.shape[1] - out.shape[1]
print(
f"{n_removed} variables with less than {minimum_reads} reads (filter_type:{filter_type})"
f"{n_removed} variables with less than {minimum_reads} reads (filter_type: '{filter_type}')"
)

adata.var['low_count'] = ~adata.var.index.isin(out.var.index.to_list())