inclusive density threshold

medema-group · Dec 12, 2024 · 39141cf · 39141cf
1 parent fdbf1b9
commit 39141cf
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diff --git 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
@@ -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(