From 575b87bbdb5b1cbda6cf73b60ead910f1734b9e6 Mon Sep 17 00:00:00 2001 From: Nick Croucher Date: Fri, 15 Nov 2024 09:45:58 +0000 Subject: [PATCH] Revert node labelling --- PopPUNK/visualise.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/PopPUNK/visualise.py b/PopPUNK/visualise.py index c067ebc7..cd58e481 100644 --- a/PopPUNK/visualise.py +++ b/PopPUNK/visualise.py @@ -699,7 +699,7 @@ def generate_visualisations(query_db, if gpu_graph: genomeNetwork = cugraph_to_graph_tool(genomeNetwork, isolateNameToLabel(all_seq)) # Hard delete from network to remove samples (mask doesn't work neatly) - if include_files is not None and not use_partial_query_graph: + if include_files is not None: genomeNetwork = remove_nodes_from_graph(genomeNetwork, all_seq, viz_subset, use_gpu = gpu_graph) elif rank_fit is not None: genomeNetwork = sparse_mat_to_network(sparse_mat, combined_seq, use_gpu = gpu_graph) @@ -708,8 +708,7 @@ def generate_visualisations(query_db, sys.exit(1) # If network has been pruned then only use the appropriate subset of names - otherwise use all names # for full network - node_labels = viz_subset if (use_partial_query_graph is not None or include_files is not None) \ - else combined_seq + node_labels = viz_subset if use_partial_query_graph is not None else combined_seq sys.stderr.write('Preparing outputs for cytoscape\n') outputsForCytoscape(genomeNetwork, mst_graph,