Make logic consistent for partial graphs

PopPUNK/plot.py

@@ -511,7 +511,7 @@ def drawMST(mst, outPrefix, isolate_clustering, clustering_name, overwrite):
                     output=graph2_file_name, output_size=(3000, 3000))
 
 def outputsForCytoscape(G, G_mst, isolate_names, clustering, outPrefix, epiCsv, queryList = None,
-                        suffix = None, writeCsv = True, use_partial_query_graph = False):
+                        suffix = None, writeCsv = True, use_partial_query_graph = None):
     """Write outputs for cytoscape. A graphml of the network, and CSV with metadata
 
     Args:
@@ -536,8 +536,8 @@ def outputsForCytoscape(G, G_mst, isolate_names, clustering, outPrefix, epiCsv,
             (default = None)
         writeCsv (bool)
             Whether to print CSV file to accompany network
-        use_partial_query_graph (bool)
-            Whether to optimise output for outputting only partial graphs
+        use_partial_query_graph (str)
+            File listing sequences to be included in output graph
     """
 
     # Avoid circular import
@@ -556,7 +556,7 @@ def outputsForCytoscape(G, G_mst, isolate_names, clustering, outPrefix, epiCsv,
     else:
         suffix = suffix + '_cytoscape'
     if use_partial_query_graph is None:
-      save_network(G, prefix = outPrefix, suffix = suffix, use_graphml = True)
+        save_network(G, prefix = outPrefix, suffix = suffix, use_graphml = True)
 
     # Save each component too (useful for very large graphs)
     component_assignments, component_hist = gt.label_components(G)