Comparative profiles too, from phylo trees

proost · Nov 29, 2017 · 9f7aff0 · 9f7aff0
1 parent 82b9f84
commit 9f7aff0
Show file tree

Hide file tree

Showing 4 changed files with 17 additions and 7 deletions.
diff --git a/conekt/controllers/heatmap.py b/conekt/controllers/heatmap.py
@@ -105,12 +105,11 @@ def heatmap_comparative_tree(tree_id, option='raw'):
 
     heatmap_data = CrossSpeciesExpressionProfile().get_heatmap(*sequence_ids, option=option)
 
-    print(heatmap_data)
-
     return render_template("expression_heatmap.html", order=heatmap_data['order'],
                            profiles=heatmap_data['heatmap_data'],
                            zlog=1 if option == 'zlog' else 0,
-                           raw=1 if option == 'raw' else 0)
+                           raw=1 if option == 'raw' else 0,
+                           tree=tree)
 
 
 @heatmap.route('/inchlib/j/<cluster_id>.json')

diff --git a/conekt/models/expression/cross_species_profile.py b/conekt/models/expression/cross_species_profile.py
@@ -93,7 +93,7 @@ def get_heatmap(self, *sequence_ids, option='raw'):
                 'sequence_id': d['sequence_id'],
                 'name': d['sequence_name'],
                 'shortest_alias': d['shortest_alias'],
-                'values': {k: v if v is not None else '-' for k,v in d['profile'][key].items()}
+                'values': {k: v if v is not None else '-' for k, v in d['profile'][key].items()}
             })
 
         return output
diff --git a/conekt/templates/expression_heatmap.html b/conekt/templates/expression_heatmap.html
@@ -43,15 +43,25 @@ <h1>Heatmap: <strong><a href="{{ url_for('expression_cluster.expression_cluster_
                 <span class="text-muted">(<i class="fa fa-flask" aria-hidden="true"></i> <em>Experimental feature, still under development</em>)</span></p>
             </div>
         </div>
+    {% elif tree %}
+        <h1>Comparative Heatmap for <a href="{{ url_for('tree.tree_view', tree_id=tree.id) }}">{{ tree.label }}</a></h1>
     {% else %}
         <h1>Heatmap</h1>
     {% endif %}
     {% if zlog == 1 %}
     <p class="text-muted" >(Values are log<sub>2</sub> transformed ratios of a genes expression in a sample divided by the mean expression level)</p>
     {% elif raw == 1 %}
-    <p class="text-muted" >(Showing raw values)</p>
+        {% if tree %}
+            <p class="text-muted" >(Showing raw values, normalize by <a href="{{ url_for('heatmap.heatmap_comparative_tree', tree_id=tree.id, option='row') }}">row</a>)</p>
+        {% else %}
+            <p class="text-muted" >(Showing raw values)</p>
+        {% endif%}
     {% else %}
-    <p class="text-muted" >(Values are normalized against highest expression of the row)</p>
+        {% if tree %}
+            <p class="text-muted" >(Values are normalized against highest expression of the row, show <a href="{{ url_for('heatmap.heatmap_comparative_tree', tree_id=tree.id, option='raw') }}">raw</a> values)</p>
+        {% else %}
+            <p class="text-muted" >(Values are normalized against highest expression of the row)</p>
+        {% endif %}
     {% endif %}
     <div class="row">
         <div class="col-lg-12">

diff --git a/conekt/templates/tree.html b/conekt/templates/tree.html
@@ -50,7 +50,8 @@ <h1><strong><em>Tree Methods</em></strong></h1>
             <li><strong>{{ tree.label }}</strong></li>
         </ol>
      <h1>{{ tree.label }}: <strong>{{ tree.method.description }}</strong></h1>
-     <p>Tree for gene family <a href="{{ url_for('family.family_view', family_id=tree.family.id) }}">{{ tree.family.name }}</a></p>
+     <p>Tree for gene family <a href="{{ url_for('family.family_view', family_id=tree.family.id) }}">{{ tree.family.name }}</a>.
+         <span class="pull-right">View expression as heatmap: <a href="{{ url_for('heatmap.heatmap_comparative_tree', tree_id=tree.id, option='raw') }}">raw</a> <span class="text-muted">|</span> <a href="{{ url_for('heatmap.heatmap_comparative_tree', tree_id=tree.id, option='row') }}">row-normalized</a></span></p>
     {% if tree.phyloxml %}
     <div class="row">
         <div class="col-lg-12">