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Fix tfidf using the wrong layer #147

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Oct 17, 2024
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Fix tfidf using the wrong layer #147

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4 changes: 2 additions & 2 deletions muon/_atac/preproc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,14 +96,14 @@ def tfidf(
tf = np.dot(n_peaks, counts)
else:
n_peaks = np.asarray(counts.sum(axis=1)).reshape(-1, 1)
tf = adata.X / n_peaks
tf = counts / n_peaks

if scale_factor is not None and scale_factor != 0 and scale_factor != 1:
tf = tf * scale_factor
if log_tf:
tf = np.log1p(tf)

idf = np.asarray(adata.shape[0] / adata.X.sum(axis=0)).reshape(-1)
idf = np.asarray(adata.shape[0] / counts.sum(axis=0)).reshape(-1)
if log_idf:
idf = np.log1p(idf)

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