diff --git a/big_scape/config.yml b/big_scape/config.yml index d94c9727..d8f10b94 100644 --- a/big_scape/config.yml +++ b/big_scape/config.yml @@ -54,11 +54,11 @@ EXTEND_GAP_SCORE: -2 # as a percentage of total domains present in the compared record. EXTEND_MAX_MATCH_PERC: 0.1 -# CLUSTER +# GCF Calling # Internal parameter of the Affinity Propagation clustering algorithm, governs the number # of families created. Higher preference will result in more families and vice versa. PREFERENCE: 0.0 -# Connected component density threshold and Affinity Propagation preference to be used +# Connected component density threshold (incl.) and Affinity Propagation preference to be used # on dense connected components. DENSITY: 0.85 DENSE_PREFERENCE: -5.0 diff --git a/big_scape/network/families.py b/big_scape/network/families.py index 2bc9108c..10a54ba4 100644 --- a/big_scape/network/families.py +++ b/big_scape/network/families.py @@ -50,7 +50,7 @@ def generate_families( similarity_matrix, node_ids = edge_list_to_sim_matrix(connected_component) - if get_cc_density(connected_component) > BigscapeConfig.DENSITY: + if get_cc_density(connected_component) >= BigscapeConfig.DENSITY: # if a connected component is highly connected, no (or less) splitting is needed # run affinity propagation with a lower preference to find the best family center labels, centers = aff_sim_matrix(