Added option to export permutation results for mapping page

Added data_scale to dataset objects and basic stats table will now check data scale when calculating range

Made interval analyst results table work with datatables

Changed the appearance of the basic stats table some by giving it a border

7 files changed, 65 insertions, 9 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index fa439b55..c0bfd70b 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -79,6 +79,8 @@ 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
@@ -125,13 +127,14 @@ 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"
@@ -278,6 +281,8 @@ 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,
             )
         
 
@@ -683,6 +688,7 @@ 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 2d4c952a..156510bb 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -153,6 +153,7 @@ 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 7f269048..d86d981e 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 3bf64a18..3cdb9339 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -265,6 +265,29 @@ 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():