Added export function for profiles

planet/controllers/profile_comparison.py

@@ -1,11 +1,12 @@
 import json
+import base64
 
 from flask import Blueprint, request, render_template,flash
 from sqlalchemy.orm import noload
 
 from planet import cache
 from planet.forms.profile_comparison import ProfileComparisonForm
-from planet.helpers.chartjs import prepare_profiles
+from planet.helpers.chartjs import prepare_profiles, prepare_profiles_download
 from planet.models.expression.coexpression_clusters import CoexpressionCluster
 from planet.models.expression.profiles import ExpressionProfile
 from planet.models.relationships.sequence_cluster import SequenceCoexpressionClusterAssociation
@@ -84,10 +85,14 @@ def profile_comparison_main():
         if len(profiles) > 50:
             flash("To many profiles in this cluster only showing the first 50", 'warning')
 
+        # Get json object for chart
         profile_chart = prepare_profiles(profiles[:50], normalize)
 
+        # Get table in base64 format for download
+        data = base64.encodebytes(prepare_profiles_download(profiles[:50], normalize).encode('utf-8'))
+
         return render_template("expression_profile_comparison.html",
-                               profiles=json.dumps(profile_chart), form=form)
+                               profiles=json.dumps(profile_chart), form=form, data=data.decode('utf-8'))
     else:
         profiles = ExpressionProfile.query.filter(ExpressionProfile.sequence_id is not None).order_by(ExpressionProfile.species_id).limit(5).all()
 

planet/helpers/chartjs.py

@@ -4,6 +4,38 @@
 from utils.color import __COLORS_RGBA as COLORS
 
 
+def prepare_profiles_download(profiles, normalize=False):
+    """
+    Function to convert a list of NetworkProfiles to a dict compatible with chart.js
+
+    :param profiles: list of profiles to include in the plot
+    :param normalize: normalize the profiles (the max value of each profile is scaled to 1)
+
+    :return dict with plot compatible with Chart.js
+    """
+    labels = []
+
+    if len(profiles) > 0:
+        data = json.loads(profiles[0].profile)
+        labels = data['order']
+
+    # initiate output array with header
+    output = ['genes\t' + '\t'.join(labels)]
+
+    for count, p in enumerate(profiles):
+        data = json.loads(p.profile)
+        expression_values = [mean(data['data'][label]) for label in labels]
+        label = p.probe if p.sequence_id is None else p.sequence.name
+
+        if normalize:
+            max_expression = max(expression_values)
+            expression_values = [value/max_expression for value in expression_values]
+
+        output.append(label + '\t' + '\t'.join(str(e) for e in expression_values))
+
+    return '\n'.join(output)
+
+
 def prepare_profiles(profiles, normalize=False):
     """
     Function to convert a list of NetworkProfiles to a dict compatible with chart.js

planet/templates/expression_profile_comparison.html

@@ -41,6 +41,12 @@ <h1>Profile comparison</h1>
     <div id="canvas-holder" class="center-block">
         <canvas id="chart-line" class="center-block" width="800" height="600"/>
     </div>
+        {% if data %}
+        <div>
+            <a class="btn btn-primary pull-right" href="data:text/plain;base64,{{data}}" download="profile_data.txt">Download</a>
+            <br />
+        </div>
+        {% endif %}
     {% else %}
     <ol class="breadcrumb">
         <li><a href="{{ url_for('main.screen') }}">Home</a></li>