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

6 files changed, 101 insertions, 19 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 6a120325..63a7a555 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -110,6 +110,17 @@ class CorrelationResults(object):
                 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.min_location_chr = start_vars['min_loc_chr']
+            self.max_location_chr = start_vars['max_loc_chr']
+            if start_vars['min_loc_mb'].isdigit():
+                self.min_location_mb = start_vars['min_loc_mb']
+            else:
+                self.min_location_mb = 0
+            if start_vars['max_loc_mb'].isdigit():
+                self.max_location_mb = start_vars['max_loc_mb']
+            else:
+                self.max_location_mb = 1000
+            self.max_location = [start_vars['max_loc_chr'], start_vars['max_loc_mb']]
             self.get_formatted_corr_type()
             self.return_number = int(start_vars['corr_return_results'])
 
@@ -167,15 +178,35 @@ class CorrelationResults(object):
                                                                        key=lambda t: -abs(t[1][0])))
 
 
+            #ZS: Convert min/max chromosome to an int for the location range option
+            min_chr_as_int = 1
+            max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing
+            for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                if chr_info.name == self.min_location_chr:
+                    min_chr_as_int = order_id
+                if chr_info.name == self.max_location_chr:
+                    max_chr_as_int = order_id
+
             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)
+                
+                #ZS: Convert trait chromosome to an int for the location range option
+                chr_as_int = 0
+                for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                    if chr_info.name == trait_object.chr: 
+                        chr_as_int = order_id
+
                 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):
+                    float(self.correlation_data[trait][0]) < self.p_range_upper and
+                    chr_as_int >= min_chr_as_int and
+                    chr_as_int <= max_chr_as_int):
+    
+                    if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)):
+                        continue
+                    elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)):
+                        continue
 
                     (trait_object.sample_r,
                     trait_object.sample_p,
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index e83437ab..850c99a7 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -139,9 +139,12 @@ class ShowTrait(object):
         self.temp_uuid = uuid.uuid4()
 
         self.sample_group_types = OrderedDict()
-        self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only"
-        self.sample_group_types['samples_other'] = "Non-" + self.dataset.group.name
-        self.sample_group_types['samples_all'] = "All Cases"
+        if len(self.sample_groups) > 1:
+            self.sample_group_types['samples_primary'] = self.dataset.group.name + " Only"
+            self.sample_group_types['samples_other'] = "Non-" + self.dataset.group.name
+            self.sample_group_types['samples_all'] = "All Cases"
+        else:
+            self.sample_group_types['samples_primary'] = self.dataset.group.name
         sample_lists = [group.sample_list for group in self.sample_groups]
         print("sample_lists is:", pf(sample_lists))
         
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index 302d5ec4..1dd54e3a 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -179,13 +179,10 @@
       for (key in _ref) {
         if (!__hasProp.call(_ref, key)) continue;
         value = _ref[key];
-        console.log("aa key:", key);
-        console.log("aa value:", value);
         the_id = process_id("column", key);
         header += "<th id=\"" + the_id + "\">" + value + "</th>";
       }
       header += "</thead>";
-      console.log("windex header is:", header);
       the_rows = "<tbody>";
       for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) {
         row = Stat_Table_Rows[_i];
@@ -201,9 +198,7 @@
         for (key in _ref1) {
           if (!__hasProp.call(_ref1, key)) continue;
           value = _ref1[key];
-          console.log("apple key:", key);
           the_id = process_id(key, row.vn);
-          console.log("the_id:", the_id);
           row_line += "<td id=\"" + the_id + "\">foo</td>";
         }
         row_line += "</tr>";
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index c5921ccf..a86a149d 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -212,7 +212,7 @@
                     "buttons": [
                         'csv'
                     ],
-                    "sDom": "RZBtir",
+                    "sDom": "RZBtr",
                     "iDisplayLength": -1,
                     "autoWidth": false,
                     "bLengthChange": true,
@@ -240,7 +240,7 @@
                     "buttons": [
                         'csv'
                     ],
-                    "sDom": "RZBtir",
+                    "sDom": "RZBtr",
                     "iDisplayLength": -1,
                     "autoWidth": false,
                     "bLengthChange": true,
@@ -254,7 +254,48 @@
                     "paging": false
                 } );
                 {% endif %}
-               
+
+                console.log("SAMPLE GROUP TYPES:", js_data.sample_group_types)
+                if (Object.keys(js_data.sample_group_types).length > 1) {
+                    $('#stats_table').DataTable( {
+                        "columns": [
+                            { "bSortable": false },
+                            { "bSortable": false },
+                            { "bSortable": false },
+                            { "bSortable": false }
+                        ],
+                        "sDom": "RZtr",
+                        "iDisplayLength": -1,
+                        "autoWidth": false,
+                        "bLengthChange": true,
+                        "bDeferRender": true,
+                        "bSortClasses": false,
+                        "colResize": {
+                            "tableWidthFixed": false
+                        },
+                        "paging": false
+                    } );
+                }
+                else {
+                    $('#stats_table').DataTable( {
+                        "columns": [
+                            { "bSortable": false },
+                            { "bSortable": false }
+                        ],
+                        "sDom": "RZtr",
+                        "iDisplayLength": -1,
+                        "autoWidth": false,
+                        "bLengthChange": true,
+                        "bDeferRender": true,
+                        "bSortClasses": false,
+                        "colResize": {
+                            "tableWidthFixed": false
+                        },
+                        "paging": false
+                    } );
+
+                }
+
                 var slider = document.getElementById('p_range_slider');
                 noUiSlider.create(slider, {
                     start: [-1.0, 1.0],
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index cefe9763..65b9d08e 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -80,6 +80,20 @@
             </div>
         </div>
         <div class="form-group">
+            <label class="col-xs-1 control-label">Location</label>
+            <div class="col-xs-4 controls">
+                <span style="margin:10px;">
+                Min Chr: <input name="min_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                </span>
+                <br>
+                <span style="margin:10px;">
+                Max Chr: <input name="max_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                Mb: <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                </span>
+            </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">
diff --git a/wqflask/wqflask/templates/show_trait_statistics_new.html b/wqflask/wqflask/templates/show_trait_statistics_new.html
index b7323ba3..1932d968 100755
--- a/wqflask/wqflask/templates/show_trait_statistics_new.html
+++ b/wqflask/wqflask/templates/show_trait_statistics_new.html
@@ -24,10 +24,8 @@
             <div class="tab-content">
                 <div class="tab-pane active" id="stats_tab">
                     <div style="padding: 20px" class="form-horizontal">
-                        <div class="well">
-                            <h3>Stats</h3>
-                            <table id="stats_table" class="table table-hover"></table>
-                        </div>
+                            <table id="stats_table" style="width: 300px; float: left;" class="table table-hover table-striped"></table>
+
                     </div>
                 </div>   
                 <div class="tab-pane" id="histogram_tab">