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Small adata Error fix #616

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Small adata Error fix #616

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faa1fd5
add checks for small data errors
AlexanderCaichen Nov 16, 2023
07603b4
Remove leftover print statements and improve warning message
AlexanderCaichen Nov 17, 2023
25c3567
Merge branch 'aristoteleo:master' into small_adata_debug
AlexanderCaichen Nov 21, 2023
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Remove leftover print statements and improve warning message
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@AlexanderCaichen
AlexanderCaichen committed Nov 17, 2023
commit 07603b4c9a8ed1ce19bd60a9b71a5a2459662e99
3 changes: 0 additions & 3 deletions dynamo/preprocessing/gene_selection.py
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Expand Up @@ -237,9 +237,6 @@ def calc_dispersion_by_svr(
# This is not picked up via None checks. (Empty valid_CM leads to a divide by 0 error in get_prediction_by_svr())
# Note that simply doing `not valid_CM.toarray()` results in "truth value of array..." error due to numpy array
# `not valid_CM.toarray().tolist()` doesn't work either because a list of empty lists still gives False
print(valid_CM.shape)
print(adata)
print(adata_ori)
if valid_CM is None or valid_CM.shape[1] == 0:
main_warning("No valid_CM for layer " + layer)

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2 changes: 1 addition & 1 deletion dynamo/preprocessing/pca.py
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Expand Up @@ -244,7 +244,7 @@ def pca(
X_data = X_data[:, valid_ind]

if 0 in X_data.shape:
main_warning("No genes passed filter, aborting preprocessing.")
main_warning("No genes passed filter, ABORTING PCA REDUCTION.")
if return_all:
return adata, None, None
else:
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