diff --git a/deconvolution/main/to_d2_graph.py b/deconvolution/main/to_d2_graph.py index ba684fefb5acd470aafbe8fe02d52d7d186614a6..04cdb07ccbcb9adbc0abe9b0d19de9fdf73ac8ac 100755 --- a/deconvolution/main/to_d2_graph.py +++ b/deconvolution/main/to_d2_graph.py @@ -13,6 +13,7 @@ def parse_arguments(): parser.add_argument('--output_prefix', '-o', default="d2_graph", help="Output file prefix.") parser.add_argument('--threads', '-t', default=8, type=int, help='Number of thread to use for dgraph computation') parser.add_argument('--debug', '-d', action='store_true', help="Debug") + parser.add_argument('--edge_divergence_threshold', '-dt', default=0.25, type=float, help='Divergence threshold value to link two udgs in the d2-graph') parser.add_argument('--maxclq', '-c', action='store_true', help="Enable max clique community detection (default behaviour)") parser.add_argument('--louvain', '-l', action='store_true', help="Enable Louvain community detection instead of all max-cliques") parser.add_argument('--comtest', '-k', action='store_true', help="Enable [placeholder] community detection algorithm instead of max-cliques") @@ -64,7 +65,7 @@ def main(): d2g = d2.D2Graph(G, debug=debug, debug_path=debug_path) dprint("D2 graph object created") dprint("constructing d2 graph from barcode graph") - d2g.construct_from_barcodes(neighbor_threshold=d2_threshold, clique_mode=clique_mode, threads=args.threads) + d2g.construct_from_barcodes(neighbor_threshold=args.edge_divergence_threshold, clique_mode=clique_mode, threads=args.threads) dprint("[debug] d2 graph constructed") # d2g.save(f"{args.output_prefix}.tsv")