Store the raw data in the AnnData object

nf-core · Jan 24, 2024 · 04cee16 · 04cee16
1 parent d94db35
commit 04cee16
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/bin/st_quality_controls.qmd b/bin/st_quality_controls.qmd
@@ -49,6 +49,9 @@ st_adata = sc.read("./" + input_adata_raw)
 # Convert X matrix from csr to csc dense matrix for output compatibility:
 st_adata.X = scipy.sparse.csc_matrix(st_adata.X)
 
+# Store the raw data so that it can be used for analyses from scratch if desired
+st_adata.layers['raw'] = st_adata.X.copy()
+
 # Print the anndata object for inspection
 print("Content of the AnnData object:")
 print(st_adata)