n bins bug fixed in scgpt

openproblems-bio · Sep 9, 2024 · 9ab1d8f · 9ab1d8f
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commit 9ab1d8f
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diff --git a/notebooks/process_results.ipynb b/notebooks/process_results.ipynb
diff --git a/src/methods/single_omics/scgpt/script.py b/src/methods/single_omics/scgpt/script.py
@@ -151,7 +151,7 @@
     result_log1p_key="X_log1p",
     subset_hvg= False,  # 5. whether to subset the raw data to highly variable genes
     hvg_flavor="seurat_v3" if data_is_raw else "cell_ranger",
-    binning=n_bins,  # 6. whether to bin the raw data and to what number of bins
+    binning=n_input_bins,  # 6. whether to bin the raw data and to what number of bins
     result_binned_key="X_binned",  # the key in adata.layers to store the binned data
 )
 preprocessor(adata, batch_key="str_batch")