Merge pull request #537 from zsloan/feature/add_location_type_correlation_option

Feature/add location type correlation option

3 files changed, 42 insertions, 19 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index a36b947c..fb4dc4f4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -99,11 +99,12 @@ class CorrelationResults(object):
                 'min_loc_mb' in start_vars and
                 'max_loc_mb' in start_vars):
 
+                self.location_type = get_string(start_vars, 'location_type')
                 self.location_chr = get_string(start_vars, 'loc_chr')
                 self.min_location_mb = get_int(start_vars, 'min_loc_mb')
                 self.max_location_mb = get_int(start_vars, 'max_loc_mb')
             else:
-                self.location_chr = self.min_location_mb = self.max_location_mb = None
+                self.location_type = self.location_chr = self.min_location_mb = self.max_location_mb = None
 
             self.get_formatted_corr_type()
             self.return_number = int(start_vars['corr_return_results'])
@@ -171,23 +172,25 @@ class CorrelationResults(object):
             self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
                                                                    key=lambda t: -abs(t[1][0])))
 
-            if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-                #ZS: Convert min/max chromosome to an int for the location range option
-                range_chr_as_int = None
-                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
-                    if 'loc_chr' in start_vars:
-                        if chr_info.name == self.location_chr:
-                            range_chr_as_int = order_id
+
+            #ZS: Convert min/max chromosome to an int for the location range option
+            range_chr_as_int = None
+            for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+                if 'loc_chr' in start_vars:
+                    if chr_info.name == self.location_chr:
+                        range_chr_as_int = order_id
 
             for _trait_counter, trait in enumerate(list(self.correlation_data.keys())[:self.return_number]):
                 trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
                 if not trait_object:
                     continue
 
-                if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-                    #ZS: Convert trait chromosome to an int for the location range option
-                    chr_as_int = 0
-                    for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+                chr_as_int = 0
+                for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
+                    if self.location_type == "highest_lod":
+                        if chr_info.name == trait_object.locus_chr:
+                            chr_as_int = order_id
+                    else:
                         if chr_info.name == trait_object.chr:
                             chr_as_int = order_id
 
@@ -197,9 +200,15 @@ class CorrelationResults(object):
                     if (self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Publish") and bool(trait_object.mean):
                         if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
                             continue
-                    if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
-                        if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+
+                    if range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+                        continue
+                    if self.location_type == "highest_lod":
+                        if (self.min_location_mb != None) and (float(trait_object.locus_mb) < float(self.min_location_mb)):
+                            continue
+                        if (self.max_location_mb != None) and (float(trait_object.locus_mb) > float(self.max_location_mb)):
                             continue
+                    else:
                         if (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
                             continue
                         if (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index b8ffa8e8..2ec9d6d5 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -528,21 +528,26 @@ $('select[name=corr_type]').change(on_corr_method_change);
 
 on_dataset_change = function() {
   let dataset_type = $('select[name=corr_dataset] option:selected').data('type');
+  let location_type = $('select[name=location_type] option:selected').val();
 
   if (dataset_type == "mrna_assay"){
     $('#min_expr_filter').show();
-    $('#location_filter').show();
+    $('select[name=location_type] option:disabled').prop('disabled', false)
   }
   else if (dataset_type == "pheno"){
     $('#min_expr_filter').show();
-    $('#location_filter').hide();
+    $('select[name=location_type]>option:eq(0)').prop('disabled', true).attr('selected', false);
+    $('select[name=location_type]>option:eq(1)').prop('disabled', false).attr('selected', true);
   }
   else {
     $('#min_expr_filter').hide();
-    $('#location_filter').show();
+    $('select[name=location_type]>option:eq(0)').prop('disabled', false).attr('selected', true);
+    $('select[name=location_type]>option:eq(1)').prop('disabled', true).attr('selected', false);
   }
 }
+
 $('select[name=corr_dataset]').change(on_dataset_change);
+$('select[name=location_type]').change(on_dataset_change);
 
 submit_special = function(url) {
   $("input[name=sample_vals]").val(JSON.stringify(fetch_sample_values()))
@@ -570,7 +575,7 @@ get_table_contents_for_form_submit = function(form_id) {
 }
 
 var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
-                        'corr_return_results', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
+                        'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper']
 
 $(".corr_compute").on("click", (function(_this) {
   return function() {
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index eaa0c308..cba977ac 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -80,7 +80,16 @@
                 <input name="min_expr" value="" type="text" class="form-control min-expr-field">
             </div>
         </div>
-        <div id="location_filter" class="form-group" style="display: {% if dataset.type != 'Publish' %}block{% else %}none{% endif %};">
+        <div class="form-group">
+            <label for="location_type" class="col-xs-2 control-label">Location Type</label>
+            <div class="col-xs-4 controls">
+                <select name="location_type" class="form-control">
+                    <option value="gene" {% if dataset.type == 'Publish' %}disabled{% endif %}>Gene</option>
+                    <option value="highest_lod">Highest LOD</option>
+                </select>
+            </div>
+        </div>
+        <div id="location_filter" class="form-group">
               <label class="col-xs-2 control-label">Location</label>
               <div class="col-xs-6 controls">
                   <span>