set n_pcs to none

panpipes/python_scripts/batch_correct_none.py

@@ -92,19 +92,18 @@
 
 if dimred not in adata.obsm:
     L.warning("Dimred '%s' could not be found in adata.obsm. Computing PCA with default parameters." % dimred)
-    n_pcs = 50
-    if adata.var.shape[0] < n_pcs:
-        L.info("You have less features than number of PCs you intend to calculate")
-        n_pcs = adata.var.shape[0] - 1
-        L.info("Setting n PCS to %i" % int(n_pcs))    
+    #n_pcs = 50
+    #if adata.var.shape[0] < n_pcs:
+    #    L.info("You have less features than number of PCs you intend to calculate")
+    #    n_pcs = adata.var.shape[0] - 1
+    #    L.info("Setting n PCS to %i" % int(n_pcs))    
     L.info("Scaling data")
     sc.pp.scale(adata)
     L.info("Computing PCA")
-    sc.tl.pca(adata, n_comps=n_pcs, 
-                    svd_solver='arpack', 
+    sc.tl.pca(adata, svd_solver='arpack', 
                     random_state=0) 
     pc_kwargs['use_rep'] = "X_pca"
-    pc_kwargs['n_pcs'] = n_pcs
+    #pc_kwargs['n_pcs'] = n_pcs
 
 
 L.info("Computing neighbors")