diff --git a/conekt/controllers/ecc.py b/conekt/controllers/ecc.py
index e974801..e248820 100644
--- a/conekt/controllers/ecc.py
+++ b/conekt/controllers/ecc.py
@@ -82,6 +82,26 @@ def ecc_graph_pair_json(ecc_id):
"""
network, family = SequenceSequenceECCAssociation.get_ecc_pair_network(ecc_id)
+ network_cytoscape = CytoscapeHelper.parse_network(network)
+ network_cytoscape = CytoscapeHelper.add_descriptions_nodes(network_cytoscape)
+ network_cytoscape = CytoscapeHelper.add_family_data_nodes(network_cytoscape, family)
+ network_cytoscape = CytoscapeHelper.add_lc_data_nodes(network_cytoscape)
+ network_cytoscape = CytoscapeHelper.add_species_data_nodes(network_cytoscape)
+ network_cytoscape = CytoscapeHelper.connect_homologs(network_cytoscape)
+
+ return json.dumps(network_cytoscape)
+
+
+@ecc.route('/multi_json/')
+def ecc_graph_multi_json():
+ """
+ Returns a JSON object compatible with cytoscape.js that contains the ECC graph for a specific pair of sequences
+
+ :param ecc_id: internal ID of the sequence to sequence ECC relationship
+ :return: JSON object compatible with cytoscape.js
+ """
+ network, family = SequenceSequenceECCAssociation.get_ecc_multi_network(2, [230458, 35796, 162930])
+
network_cytoscape = CytoscapeHelper.parse_network(network)
network_cytoscape = CytoscapeHelper.add_descriptions_nodes(network_cytoscape)
network_cytoscape = CytoscapeHelper.add_family_data_nodes(network_cytoscape, family)
diff --git a/conekt/helpers/cytoscape.py b/conekt/helpers/cytoscape.py
index eeff254..57aead8 100644
--- a/conekt/helpers/cytoscape.py
+++ b/conekt/helpers/cytoscape.py
@@ -251,6 +251,28 @@ def add_depth_data_nodes(network):
return colored_network
+ @staticmethod
+ def connect_homologs(network):
+ connected_network = deepcopy(network)
+ """
+ Add edges between homologous genes from different targets, family_id needs to be specified !
+ """
+
+ for i in range(len(connected_network['nodes']) - 1):
+ for j in range(i + 1, len(connected_network['nodes'])):
+ if connected_network['nodes'][i]['data']['family_id'] == connected_network['nodes'][j]['data']['family_id'] and connected_network['nodes'][i]['data']['family_id'] is not None:
+ connected_network['edges'].append({
+ 'data': {'source': connected_network['nodes'][i]['data']['id'],
+ 'target': connected_network['nodes'][j]['data']['id'],
+ 'color': "#33D",
+ 'homology_color': "#33D",
+ 'edge_type': 'homology',
+ 'ecc_pair_color': "#33D",
+ 'homology': True}
+ })
+
+ return connected_network
+
@staticmethod
def add_connection_data_nodes(network):
"""
diff --git a/conekt/models/relationships/sequence_sequence_ecc.py b/conekt/models/relationships/sequence_sequence_ecc.py
index 7363aa6..c1bf778 100644
--- a/conekt/models/relationships/sequence_sequence_ecc.py
+++ b/conekt/models/relationships/sequence_sequence_ecc.py
@@ -201,32 +201,47 @@ def get_ecc_pair_network(ecc_id):
"edge_type": "expression",
'ecc_pair_color': "#3D3"})
- """
- Add gene families to sequences
- """
- seq_fams = SequenceFamilyAssociation.query.filter(and_(SequenceFamilyAssociation.sequence_id.in_(sequences),
- SequenceFamilyAssociation.family.has(method_id=association.gene_family_method_id)
- )).all()
-
- seq_to_fam = {sf.sequence_id: sf.gene_family_id for sf in seq_fams}
+ return {"nodes": nodes, "edges": edges}, association.gene_family_method_id
- for i, node in enumerate(nodes):
- nodes[i]['family_id'] = seq_to_fam[node['gene_id']] if node['gene_id'] in seq_to_fam.keys() else None
-
- """
- Add edges between homologous genes from different targets
- """
-
- for i in range(len(nodes) - 1):
- for j in range(i + 1, len(nodes)):
- if nodes[i]['family_id'] == nodes[j]['family_id'] and nodes[i]['family_id'] is not None:
- edges.append(
- {'source': nodes[i]['id'],
- 'target': nodes[j]['id'],
- 'homology_color': "#33D",
- 'edge_type': 'homology',
- 'ecc_pair_color': "#33D",
- 'homology': True}
- )
-
- return {"nodes": nodes, "edges": edges}, association.gene_family_method_id
\ No newline at end of file
+ @staticmethod
+ def get_ecc_multi_network(gf_method_id, sequence_ids):
+ associations = SequenceSequenceECCAssociation.query.\
+ filter(SequenceSequenceECCAssociation.gene_family_method_id == gf_method_id).\
+ filter(and_(SequenceSequenceECCAssociation.query_id.in_(sequence_ids),
+ SequenceSequenceECCAssociation.target_id.in_(sequence_ids))).\
+ all()
+
+ nodes = []
+ edges = []
+ node_sequence_ids = []
+
+ for a in associations:
+ if a.query_id not in node_sequence_ids:
+ node_sequence_ids.append(a.query_id)
+ nodes.append({"id": a.query_sequence.name,
+ "name": a.query_sequence.name,
+ "species_id": a.query_sequence.species_id,
+ "species_name": a.query_sequence.species.name,
+ "gene_id": a.query_id,
+ "gene_name": a.query_sequence.name,
+ "network_method_id": a.query_network_method_id,
+ "node_type": "query"})
+
+ if a.target_id not in node_sequence_ids:
+ node_sequence_ids.append(a.target_id)
+ nodes.append({"id": a.target_sequence.name,
+ "name": a.target_sequence.name,
+ "species_id": a.target_sequence.species_id,
+ "species_name": a.target_sequence.species.name,
+ "gene_id": a.target_id,
+ "gene_name": a.target_sequence.name,
+ "network_method_id": a.target_network_method_id,
+ "node_type": "query"})
+
+ edges.append({"source": a.query_sequence.name,
+ "target": a.target_sequence.name,
+ "ecc_score": a.ecc,
+ 'ecc_pair_color': "#D33",
+ "edge_type": "ecc"})
+
+ return {"nodes": nodes, "edges": edges}, gf_method_id
diff --git a/conekt/templates/expression_graph.html b/conekt/templates/expression_graph.html
index e8f930c..ea5d569 100644
--- a/conekt/templates/expression_graph.html
+++ b/conekt/templates/expression_graph.html
@@ -111,7 +111,7 @@ ECC pair
{% if sequence %}
ECC
{% endif %}
- {% if not sequence %}
+ {% if not sequence and not ecc_pair %}
Cutoff: {{cutoff}}