added low abundance warning on profile pages

proost · Sep 19, 2017 · 02a3a6a · 02a3a6a
1 parent 8e6e4cc
commit 02a3a6a
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Showing 3 changed files with 25 additions and 0 deletions.
diff --git a/planet/models/expression/profiles.py b/planet/models/expression/profiles.py
@@ -63,6 +63,20 @@ def tissue_table(self, condition_tissue_id, use_means=True):
                                                      )
         return table
 
+    @property
+    def low_abundance(self, cutoff=10):
+        """
+        Checks if the mean expression value in any conditions in the plot is higher than the desired cutoff
+
+        :param cutoff: cutoff for expression, default = 10
+        :return: True in case of low abundance otherwise False
+        """
+        data = json.loads(self.profile)
+
+        checks = [mean(v) > cutoff for _, v in data["data"].items()]
+
+        return not any(checks)
+
     def tissue_profile(self, condition_tissue_id, use_means=True):
         """
         Applies a conversion to the profile, grouping several condition into one more general feature (e.g. tissue).

diff --git a/planet/static/css/main.css b/planet/static/css/main.css
@@ -519,4 +519,8 @@ div#phyd3 .table-responsive > table {
 
 .global-message {
         color: #31708f;
+}
+
+.warning-message {
+        color: #a94442;
 }
diff --git a/planet/templates/expression_profile.html b/planet/templates/expression_profile.html
@@ -32,11 +32,18 @@ <h1>Expression profile for <strong><a href="{{url_for('sequence.sequence_view',
     <h1>Expression profile for: <strong>{{ profile.probe }}</strong></h1>
     {% endif %}
 
+    {% if profile.low_abundance %}
+    <br />
+    <span class="warning-message"><i class="fa fa-exclamation-triangle" aria-hidden="true"></i> <strong>Attention:</strong> This gene has <strong>low abundance</strong>.</span>
+    <br /><br />
+    {% endif %}
+
     {% for s in profile.specificities %}
     <span>{{ s.method.description }}: <strong>{{ s.condition }}</strong> (<abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='spm') }}" data-target="#helpModal">SPM</abbr>: {{ s.score|round(2) }},
         <abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='entropy') }}" data-target="#helpModal">entropy</abbr>: {{ s.entropy|round(2) }}{%- if s.tau -%}, <abbr title="Click to show help" href="{{ url_for('help.help_topic', topic='tau') }}" data-target="#helpModal">tau</abbr>: {{ s.tau|round(2) }}{% endif %})</span><br />
     {% endfor %}
 
+
     <br/>
     <div class="row">
         <div class="col-lg-12 col-md-12 col-sm-12">