Neighborhood comparisons are now better. Show intersection only is po…

…ssible.

README.md

@@ -26,7 +26,7 @@ Tutorials
   * [Coexpression Networks and Clusters](docs/tutorials/005_coexpression_networks_clusters.md)
 
 
-Anything missing ? Further questions ? Don't hesitate to [contact](mailto:proost@mpimp-golm.mpg.de) us.
+Anything missing ? Further questions ? Don't hesitate to [contact](mailto:sebastian.proost@gmail.com) us.
 
 Setting up CoNekT
 -----------------
@@ -56,5 +56,5 @@ Contact
 -------
 
   * [Marek Mutwil](mailto:mutwil@mpmpi-golm.mpg.de) ( mutwil@mpmpi-golm.mpg.de )
-  * [Sebastian Proost](mailto:proost@mpimp-golm.mpg.de) ( proost@mpimp-golm.mpg.de )
+  * [Sebastian Proost](mailto:sebastian.proost@gmail.com) ( sebastian.proost@gmail.com )
 

conekt/controllers/ecc.py

@@ -101,6 +101,7 @@ def ecc_graph_pair_json(ecc_id):
     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)
+    network_cytoscape = CytoscapeHelper.tag_ecc_singles(network_cytoscape)
 
     return json.dumps(network_cytoscape)
 

conekt/helpers/cytoscape.py

@@ -455,6 +455,65 @@ def prune_unique_lc(network):
 
         return pruned_network
 
+    @staticmethod
+    def tag_ecc_singles(network):
+        """
+        When comparing ECC pairs, genes without a homolog in the graph could be hidden, to this end these genes need
+        to be tagged so javascript can handle this.
+
+        :param network: input network
+        :return: network with singles tagged
+        """
+        output_network = deepcopy(network)
+
+        # Find Query genes, add hideable tag to everything except queries
+        queries = []
+        for n in output_network['nodes']:
+                if n['data']['node_type'] == 'query' and n['data']['name'] not in queries:
+                    queries.append(n['data']['name'])
+                    n['data']['tag'] = 'always_show'
+                else:
+                    n['data']['tag'] = 'hideable'
+
+        # Store neighborhoods
+        neighborhoods = {q: [] for q in queries}
+
+        for e in output_network['edges']:
+            if e['data']['source'] in queries:
+                if e['data']['target'] not in queries:
+                    neighborhoods[e['data']['source']].append(e['data']['target'])
+            elif e['data']['target'] in queries:
+                if e['data']['source'] not in queries:
+                    neighborhoods[e['data']['target']].append(e['data']['source'])
+
+        # adjust tags on genes that should be shown (shared neighborhood)
+        # Check for genes present in both neighborhoods (intra species comparisons)
+        for n in output_network['nodes']:
+            counter = 0
+            for k in queries:
+                if n['data']['name'] in neighborhoods[k]:
+                    counter += 1
+            if counter > 1:
+                n['data']['tag'] = 'always_show'
+
+        # Check homology edges
+        genes_to_show = []
+        for e in output_network['edges']:
+            if 'homology' in e['data'].keys() and e['data']['homology']:
+                counter = 0
+                for k in queries:
+                    if e['data']['source'] in neighborhoods[k] or e['data']['target'] in neighborhoods[k]:
+                        counter += 1
+                if counter > 1:
+                    genes_to_show.append(e['data']['source'])
+                    genes_to_show.append(e['data']['target'])
+
+        for n in output_network['nodes']:
+            if n['data']['name'] in genes_to_show:
+                n['data']['tag'] = 'always_show'
+
+        return output_network
+
     @staticmethod
     def merge_networks(network_one, network_two):
         """

conekt/static/js/cytoscape.cycss

@@ -35,6 +35,10 @@ node:selected {
         line-color: black;
 }
 
+node.hidden {
+    visibility: hidden;
+}
+
 node.found {
         width: 50px;
         height: 60px;
@@ -177,4 +181,8 @@ edge.default_width {
 
 edge.depth {
         width: mapData(depth, 0, 2, 3, 1);
+}
+
+edge.hidden {
+    visibility: hidden;
 }

conekt/static/js/planet_graph.js

@@ -390,6 +390,20 @@ $(function () { // on dom ready
         cy.nodes('[^compound]').addClass($(this).attr('attr'));
     });
 
+    $('.cy-node-hide').click(function (ev) {
+        ev.preventDefault();
+        cy.nodes('[tag="hideable"]').addClass('hidden');
+        $(this).hide();
+        $('.cy-node-show').show();
+    });
+
+    $('.cy-node-show').click(function (ev) {
+        ev.preventDefault();
+        cy.nodes('[tag="hideable"]').removeClass('hidden');
+        $(this).hide();
+        $('.cy-node-hide').show();
+    });
+
     $('.cy-edge-color').click(function (ev) {
         ev.preventDefault();
         $(this).closest('.cy-option-menu').find('.cy-edge-color').each(function () {

conekt/templates/expression_graph.html

@@ -62,13 +62,13 @@ <h1>ECC multi</h1>
                                     {% if node %}
                                     <li><a href="#" class="cy-node-color" attr="depth_color">Depth</a></li>
                                     {% endif %}
-                                    <li><a href="#" class="cy-node-color" attr="family_color">Family <span class="text-muted">(default)</span></a></li>
+                                    <li><a href="#" class="cy-node-color" attr="family_color">Family {%- if not (ecc_pair or ecc_multi) -%} <span class="text-muted">(default)</span>{%- endif -%}</a></li>
                                     <li><a href="#" class="cy-node-color" attr="lc_color">Label Co-occ.</a></li>
                                     {% if cluster or cluster_one %}
                                     <li><a href="#" class="cy-node-color" attr="neighbors">Neighbors</a></li>
                                     {% endif %}
                                     {% if sequence or ecc_pair or ecc_multi %}
-                                    <li><a href="#" class="cy-node-color" attr="species_color">Species</a></li>
+                                    <li><a href="#" class="cy-node-color" attr="species_color">Species {%- if ecc_pair or ecc_multi -%} <span class="text-muted">(default)</span>{%- endif -%}</a></li>
                                     {% endif %}
                                     {% if graph_data %}
                                     <li><a href="#" class="cy-node-color" attr="spm_color">Specificity</a></li>
@@ -85,6 +85,11 @@ <h1>ECC multi</h1>
                                         <li><a href="#" class="cy-node-shape" attr="spm_shape">Specificity</a></li>
                                         {% endif %}
                                     </div>
+                                    {% if ecc_pair %}
+                                    <li><hr /></li>
+                                    <li class="dropdown-header">Neighborhood comparison</li>
+                                    <li><a href="#" class="cy-node-hide">Show Only Intersection</a><a href="#" class="cy-node-show" style="display:none">Show All</a></li>
+                                    {% endif %}
                                 </ul>
                             </div>
                             <div class="dropdown btn-group" role="group">