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🐛 Small fix for bug in compensation function. #39

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Merged
mbuttner merged 2 commits into from
Jun 8, 2023
Merged

🐛 Small fix for bug in compensation function. #39

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015b521
Fixed issue with no indices intersecting and not catching it and add…
ricomnl May 30, 2023
b0cbb25
ran pre-commit
ricomnl Jun 3, 2023
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14 changes: 12 additions & 2 deletions pytometry/preprocessing/_process_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -151,11 +151,11 @@ def compensate(
# the compensation matrix may have different index names than the adata.X matrix
ref_col = adata.var.index
idx_in = np.intersect1d(compens.columns, ref_col)
if idx_in is None:
if not idx_in.any():
# try the adata.var['channel'] as reference
ref_col = adata.var["channel"]
idx_in = np.intersect1d(compens.columns, ref_col)
if idx_in is None:
if not idx_in.any():
raise ValueError(
"Could not match the column names of the compensation matrix"
'with neither `adata.var.index` nor `adata.var["channel"].'
Expand All @@ -172,7 +172,17 @@ def compensate(
# sort compensation matrix by adata.var_names
compens = compens.iloc[idx_sort, idx_sort]
X_comp = np.linalg.solve(compens.T, adata.X[:, ref_idx].T).T

X = adata.X.copy()
adata.X[:, ref_idx] = X_comp

if np.array_equal(X, adata.X):
print(
"Compensation failed - matrices before and after are equivalent. Please"
" check your compensation matrix."
)
del X

# check for nan values
nan_val = np.isnan(adata.X[:, ref_idx]).sum()
if nan_val > 0:
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