Merge branch 'master' of github.com:genenetwork/genenetwork2 into WGCNAintegration

3 files changed, 72 insertions, 19 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 63631350..6a120325 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -104,6 +104,12 @@ class CorrelationResults(object):
             self.sample_data = {}
             self.corr_type = start_vars['corr_type']
             self.corr_method = start_vars['corr_sample_method']
+            if start_vars['min_expr'] == "":
+                self.min_expr = 0
+            else:
+                self.min_expr = float(start_vars['min_expr'])
+            self.p_range_lower = float(start_vars['p_range_lower'])
+            self.p_range_upper = float(start_vars['p_range_upper'])
             self.get_formatted_corr_type()
             self.return_number = int(start_vars['corr_return_results'])
 
@@ -164,27 +170,30 @@ class CorrelationResults(object):
             for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
                 print("trait name:", trait)
                 trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
+                print("trait_object.mean:", trait_object.mean)
+                print("self.min_expr:", self.min_expr)
+                print("self.p_range_upper:", self.p_range_upper)
+                if (float(trait_object.mean) > self.min_expr and 
+                    float(self.correlation_data[trait][0]) > self.p_range_lower and
+                    float(self.correlation_data[trait][0]) < self.p_range_upper):
+
+                    (trait_object.sample_r,
+                    trait_object.sample_p,
+                    trait_object.num_overlap) = self.correlation_data[trait]
                 
-                (trait_object.sample_r,
-                trait_object.sample_p,
-                trait_object.num_overlap) = self.correlation_data[trait]
-                
-                #trait_object.sample_p = self.correlation_data[trait][1]
-                #trait_object.num_overlap = self.correlation_data[trait][2]
-                
-                #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
-                #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
+                    #Get symbol for trait and call function that gets each tissue value from the database (tables TissueProbeSetXRef,
+                    #TissueProbeSetData, etc) and calculates the correlation (cal_zero_order_corr_for_tissue in correlation_functions)
                 
-                # Set some sane defaults
-                trait_object.tissue_corr = 0
-                trait_object.tissue_pvalue = 0
-                trait_object.lit_corr = 0
-                if self.corr_type == "tissue":
-                    trait_object.tissue_corr = tissue_corr_data[trait][1]
-                    trait_object.tissue_pvalue = tissue_corr_data[trait][2]
-                elif self.corr_type == "lit":    
-                    trait_object.lit_corr = lit_corr_data[trait][1]
-                self.correlation_results.append(trait_object)
+                    # Set some sane defaults
+                    trait_object.tissue_corr = 0
+                    trait_object.tissue_pvalue = 0
+                    trait_object.lit_corr = 0
+                    if self.corr_type == "tissue":
+                        trait_object.tissue_corr = tissue_corr_data[trait][1]
+                        trait_object.tissue_pvalue = tissue_corr_data[trait][2]
+                    elif self.corr_type == "lit":    
+                        trait_object.lit_corr = lit_corr_data[trait][1]
+                    self.correlation_results.append(trait_object)
 
             self.target_dataset.get_trait_info(self.correlation_results, self.target_dataset.group.species)
             
@@ -478,6 +487,7 @@ class CorrelationResults(object):
         this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(
             this_trait_vals, target_vals)
 
+        #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ 
         if self.corr_method == 'pearson':
             sample_r, sample_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
         else:
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 55464635..c5921ccf 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -12,6 +12,8 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/nvd3/nv.d3.min.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.bootstrap.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/noUiSlider/nouislider.pips.css" />
     <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
 
 {% endblock %}
@@ -147,6 +149,7 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/packages/noUiSlider/nouislider.js"></script>
     <script type="text/javascript" charset="utf-8">
             
            function getValue(x) {
@@ -251,6 +254,29 @@
                     "paging": false
                 } );
                 {% endif %}
+               
+                var slider = document.getElementById('p_range_slider');
+                noUiSlider.create(slider, {
+                    start: [-1.0, 1.0],
+                    range: {
+                        'min': [-1.0],
+                        'max': [1.0]
+                    }
+                });
+
+                var slider_display =  [
+                    document.getElementById('p_range_lower'),
+                    document.getElementById('p_range_upper')
+                ];
+                var slider_values =  [
+                    $('input[name=p_range_lower]'),
+                    $('input[name=p_range_upper]')
+                ];                
+
+                slider.noUiSlider.on('update', function( values, handle ) {
+                    slider_display[handle].innerHTML = values[handle];
+                    slider_values[handle].val(values[handle]);
+                });
             });
     </script>
     
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index f02d1705..cefe9763 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -72,6 +72,23 @@
                 </select>
             </div>
         </div>
+
+        <div class="form-group">
+            <label class="col-xs-1 control-label">Min Expr</label>
+            <div class="col-xs-2 controls">
+                <input name="min_expr" value="" type="text" class="form-control" style="width: 50px;">
+            </div>
+        </div>
+        <div class="form-group">
+            <label class="col-xs-1 control-label">Range</label>
+            <div class="col-xs-3 controls">
+                <input name="p_range_lower" value="" type="hidden">
+                <input name="p_range_upper" value="" type="hidden">
+                <div id="p_range_slider" ></div>
+                <span style="font: 400 12px Arial; color: #888; display: block; margin: 15px 0;" id="p_range_lower"></span>
+                <span style="font: 400 12px Arial; color: #888; display: block; margin: 15px 0;" id="p_range_upper"></span>
+            </div>
+        </div>
         
         <div class="form-group">
             <label for="corr_sample_method" class="col-xs-1 control-label"></label>