remove test as bbknn now works at these higher values

panpipes/funcs/plotting.py

@@ -79,7 +79,7 @@ def batch_scatter_two_var(plot_df, method, batch, palette_choice=None):
                             colour=palette_choice[i], 
                             title=str(method_choice) + "|" + str(group_choice))
                 idx+=1
-                logging.info(idx)
+                logging.debug(idx)
     return fig, axs
 
 

panpipes/python_scripts/batch_correct_bbknn.py

@@ -61,24 +61,10 @@
 
     # make sure that batch is a categorical
     adata.obs["comb_columns"] = adata.obs["comb_columns"].astype("category")
-    # test the minimum number of neighbours needed for the function to not break,
-    # the safe point is 40 in my tests
-    nn_test = nnb * len(adata.obs["comb_columns"].unique())
-    if nn_test > 40:
-        nnb = nnb - 1
-        L.info("reducing the numbers within batch to %i as the number of batches is high, \
-               and bbknn will likely crash" % nnb)
-        if nnb < 1:
-            sys.exit("can't work with 0 neighbors_within_batch")
     # run bbknn
     adata = sc.external.pp.bbknn(adata, batch_key="comb_columns", copy=True, neighbors_within_batch=nnb)
 else:
     adata.obs[args.integration_col] = adata.obs[args.integration_col].astype("category")
-    nn_test = nnb * len(adata.obs[args.integration_col].unique())
-    if nn_test > 40:
-        nnb = nnb - 1
-        if nnb < 1:
-            sys.exit("can't work with 0 neighbors_within_batch") 
     # run bbknn
     adata = sc.external.pp.bbknn(adata,
                         batch_key=args.integration_col,