Comparative profiles work for families

proost · Nov 29, 2017 · 22d7ee9 · 22d7ee9
1 parent 9f7aff0
commit 22d7ee9
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Showing 2 changed files with 27 additions and 1 deletion.
diff --git a/conekt/controllers/heatmap.py b/conekt/controllers/heatmap.py
@@ -9,6 +9,7 @@
 from conekt.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation
 from conekt.models.sequences import Sequence
 from conekt.models.trees import Tree
+from conekt.models.gene_families import GeneFamily
 from conekt.models.expression.cross_species_profile import CrossSpeciesExpressionProfile
 
 heatmap = Blueprint('heatmap', __name__)
@@ -112,6 +113,25 @@ def heatmap_comparative_tree(tree_id, option='raw'):
                            tree=tree)
 
 
+@heatmap.route('/comparative/family/<int:family_id>')
+@heatmap.route('/comparative/family/<int:family_id>/<option>')
+@cache.cached()
+def heatmap_comparative_family(family_id, option='raw'):
+    family = GeneFamily.query.get_or_404(family_id)
+    sequences = family.sequences
+    sequence_ids = [s.id for s in sequences]
+
+    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,
+                           family=family)
+
+
 @heatmap.route('/inchlib/j/<cluster_id>.json')
 @cache.cached()
 def heatmap_inchlib_json(cluster_id):

diff --git a/conekt/templates/expression_heatmap.html b/conekt/templates/expression_heatmap.html
@@ -45,6 +45,8 @@ <h1>Heatmap: <strong><a href="{{ url_for('expression_cluster.expression_cluster_
         </div>
     {% elif tree %}
         <h1>Comparative Heatmap for <a href="{{ url_for('tree.tree_view', tree_id=tree.id) }}">{{ tree.label }}</a></h1>
+    {% elif family %}
+        <h1>Comparative Heatmap for <a href="{{ url_for('family.family_view', family_id=family.id) }}">{{ family.name }}</a></h1>
     {% else %}
         <h1>Heatmap</h1>
     {% endif %}
@@ -53,12 +55,16 @@ <h1>Heatmap</h1>
     {% elif raw == 1 %}
         {% 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>
+        {% elif family %}
+            <p class="text-muted" >(Showing raw values, normalize by <a href="{{ url_for('heatmap.heatmap_comparative_family', family_id=family.id, option='row') }}">row</a>)</p>
         {% else %}
             <p class="text-muted" >(Showing raw values)</p>
         {% endif%}
     {% else %}
         {% 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>
+        {% elif family %}
+            <p class="text-muted" >(Values are normalized against highest expression of the row, show <a href="{{ url_for('heatmap.heatmap_comparative_family', family_id=family.id, option='raw') }}">raw</a> values)</p>
         {% else %}
             <p class="text-muted" >(Values are normalized against highest expression of the row)</p>
         {% endif %}
@@ -92,7 +98,7 @@ <h1>Heatmap</h1>
                     <td><div><span>{{ p.name }}</span></div></td>
                     {% endif %}
                     {% for o in order %}
-                    <td class="value">{% if p['values'][o] != '-' %}{{ p['values'][o]|round(2) }}{% else %}-{% endif %}</td>
+                    <td class="value">{% if p['values'][o] != '-' and p['values'][o] is defined %}{{ p['values'][o]|round(2) }}{% else %}-{% endif %}</td>
                     {% endfor %}
                 </tr>
             {% endfor %}