Merge

8 files changed, 68 insertions, 11 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 52ac95f0..053b45fc 100755..100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -417,6 +417,7 @@ class DataSet(object):
         self.shortname = None
         self.fullname = None
         self.type = None
+        self.data_scale = None #ZS: For example log2
 
         self.setup()
 
@@ -456,8 +457,8 @@ class DataSet(object):
                     self.name,
                     self.name))
 
-                self.id, self.name, self.fullname, self.shortname, self.tissue = g.db.execute("""
-                        SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, Tissue.Name
+                self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = g.db.execute("""
+                        SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
                         FROM ProbeSetFreeze, ProbeFreeze, Tissue
                         WHERE ProbeSetFreeze.public > %s AND
                               ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id AND
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index b56b179b..08f422f0 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -74,6 +74,8 @@ class MarkerRegression(object):
         self.pair_scan = False # Initializing this since it is checked in views to determine which template to use
         self.score_type = "LRS" #ZS: LRS or LOD
         self.mapping_scale = "physic"
+        self.num_perm = 0
+        self.perm_output = []
         self.bootstrap_results = []
         
         #ZS: This is passed to GN1 code for single chr mapping
@@ -120,13 +122,14 @@ class MarkerRegression(object):
             try:
                 if int(start_vars['num_perm']) > 0:
                     self.num_perm = int(start_vars['num_perm'])
-                else:
-                    self.num_perm = 0
             except:
                 self.num_perm = 0
             
             self.LRSCheck = self.score_type
-            self.permCheck = "ON"
+            if self.num_perm > 0:
+                self.permCheck = "ON"
+            else:
+                self.permCheck = False
             self.showSNP = "ON"
             self.showGenes = "ON"
             self.viewLegend = "ON"
@@ -273,6 +276,8 @@ class MarkerRegression(object):
                 mapping_scale = self.mapping_scale,
                 chromosomes = chromosome_mb_lengths,
                 qtl_results = self.qtl_results,
+                num_perm = self.num_perm,
+                perm_results = self.perm_output,
             )
         
 
@@ -652,6 +657,7 @@ class MarkerRegression(object):
             self.perm_output = genotype.permutation(strains = trimmed_samples, trait = trimmed_values, nperm=self.num_perm)
             self.suggestive = self.perm_output[int(self.num_perm*0.37-1)]
             self.significant = self.perm_output[int(self.num_perm*0.95-1)]
+            self.highly_significant = self.perm_output[int(self.num_perm*0.99-1)]
             
         self.json_data['suggestive'] = self.suggestive
         self.json_data['significant'] = self.significant
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 79f1c867..074c78bf 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -150,6 +150,7 @@ class ShowTrait(object):
         self.trait_table_width = get_trait_table_width(self.sample_groups)
 
         js_data = dict(dataset_type = self.dataset.type,
+                       data_scale = self.dataset.data_scale,
                        sample_group_types = self.sample_group_types,
                        sample_lists = sample_lists,
                        attribute_names = self.sample_groups[0].attributes,
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 9d418e9b..9e249c28 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -190,9 +190,9 @@
         }
         row_line = "<tr>";
         if (row.url != null) {
-          row_line += "<td id=\"" + row.vn + "\" style=\"border-right: 1px solid #000000;\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
+          row_line += "<td id=\"" + row.vn + "\"><a href=\"" + row.url + "\">" + row.pretty + "</a></td>";
         } else {
-          row_line += "<td id=\"" + row.vn + "\" style=\"border-right: 1px solid #000000;\">" + row.pretty + "</td>";
+          row_line += "<td id=\"" + row.vn + "\">" + row.pretty + "</td>";
         }
         _ref1 = js_data.sample_group_types;
         for (key in _ref1) {
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 07f764ca..df948190 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -22,6 +22,7 @@
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}">
         <input type="hidden" name="num_perm" value="{{ nperm }}">
+        <input type="hidden" name="perm_results" value="">
         <input type="hidden" name="num_bootstrap" value="{{ nboot }}">
         <input type="hidden" name="do_control" value="{{ doControl }}">
         <input type="hidden" name="control_marker" value="{{ controlLocus }}">
@@ -148,9 +149,12 @@
                   <br>
                   <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span>
                   {% endif %}
-                  {% if nperm > 0 %}
+                  {% if nperm > 0 and permChecked == "ON" %}
                   <br><br>
                   <img src="/static/output/{{ perm_filename }}.gif">
+                  <br><br>
+                  Total of {{ nperm }} permutations&nbsp;&nbsp;<a href="javascript:export_perm_data();" target="_blank" >Download Permutation Results</a>
+                  <br>
                   {% endif %}
               </div>
             </div>
@@ -292,7 +296,20 @@
                 "scrollCollapse": true,
                 "paging": false
             } );
-            console.timeEnd("Creating table");
+
+            $('#interval_analyst').dataTable( {
+                "columnDefs": [ {
+                    "targets": 0,
+                    "sortable": false
+                }],
+                "order": [[3, "asc"]],
+                "sDom": "RZtir",
+                "iDisplayLength": -1,
+                "autoWidth": true,
+                "bDeferRender": true,
+                "bSortClasses": false,
+                "paging": false
+            } );
 
             $('#vector_map_tab').click(function(){
                 $('div#gn1_map_options').hide();
@@ -325,6 +342,16 @@
             return $('#marker_regression_form').submit(); 
         };
 
+        export_perm_data = function() {
+            var num_perm, perm_data;
+            num_perm = js_data.num_perm
+            perm_data = js_data.perm_results
+            json_perm_data = JSON.stringify(perm_data);
+            $('input[name=perm_results]').val(json_perm_data);
+            $('#marker_regression_form').attr('action', '/export_perm_data');
+            return $('#marker_regression_form').submit();
+    };
+
     </script>
 
 {% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 7429cd5f..64638fc7 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -254,7 +254,6 @@
                 } );
                 {% endif %}
 
-                console.log("SAMPLE GROUP TYPES:", js_data.sample_group_types)
                 if (Object.keys(js_data.sample_group_types).length > 1) {
                     $('#stats_table').DataTable( {
                         "columnDefs": [
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index 9a57b285..242f1c26 100755
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -26,7 +26,7 @@
             <div class="tab-content">
                 <div class="tab-pane active" id="stats_tab">
                     <div style="padding: 20px" class="form-horizontal">
-                            <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped cell-border"></table>
+                            <table border="1" id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped cell-border"></table>
                     </div>
                 </div>   
                 <div class="tab-pane" id="histogram_tab">
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 87ba8b32..bd2fff50 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -284,6 +284,29 @@ def export_trait_csv():
     return Response(csv_data,
                     mimetype='text/csv',
                     headers={"Content-Disposition":"attachment;filename=sample_data.csv"})
+                    
+@app.route('/export_perm_data', methods=('POST',))
+def export_perm_data():
+    """CSV file consisting of the permutation data for the mapping results"""
+    num_perm = float(request.form['num_perm'])
+    perm_data = json.loads(request.form['perm_results'])
+    
+    buff = StringIO.StringIO()
+    writer = csv.writer(buff)
+    writer.writerow(["Suggestive LRS (p=0.63) = " + str(perm_data[int(num_perm*0.37-1)])])
+    writer.writerow(["Significant LRS (p=0.05) = " + str(perm_data[int(num_perm*0.95-1)])])
+    writer.writerow(["Highly Significant LRS (p=0.01) = " + str(perm_data[int(num_perm*0.99-1)])])
+    writer.writerow("")
+    writer.writerow([str(num_perm) + " Permutations"])
+    writer.writerow("")
+    for item in perm_data:
+        writer.writerow([item])
+    csv_data = buff.getvalue()
+    buff.close()
+
+    return Response(csv_data,
+                    mimetype='text/csv',
+                    headers={"Content-Disposition":"attachment;filename=perm_data.csv"})
 
 @app.route("/show_trait")
 def show_trait_page():