Loading screen should now show correct N when re-mapping or zooming into a map

5 files changed, 14 insertions, 11 deletions

diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 74fa4329..89f56c30 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -147,7 +147,7 @@ class DisplayMappingResults(object):
 
         self.dataset = start_vars['dataset']
         self.this_trait = start_vars['this_trait']
-        self.n_samples = start_vars['num_vals']
+        self.n_samples = start_vars['n_samples']
         self.species = start_vars['species']
         self.genofile_string = ""
         if 'genofile_string' in start_vars:
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index c859fdaa..c9d10f7c 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -124,7 +124,10 @@ class RunMapping(object):
                             self.samples.append(sample)
                             self.vals.append(value)
 
-        self.num_vals = len(self.vals)
+        if 'n_samples' in start_vars:
+            self.n_samples = start_vars['n_samples']
+        else:
+            self.n_samples = len([val for val in self.vals if val != "x"])
 
         #ZS: Check if genotypes exist in the DB in order to create links for markers
 
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index 49bcbff7..15ab4080 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -11,7 +11,7 @@
         {% if start_vars.tool_used == "Mapping" %}
         <h1>Computing the Maps</h1>
         <br>
-        <i>n</i> = {{ start_vars.num_vals }}
+        <i>n</i> = {{ start_vars.n_samples }}
         <br>
         Method = {% if start_vars.method == "gemma" %}GEMMA{% else %}{{ start_vars.method }}{% endif %}
         <br>
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index c5d49168..132d5249 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -35,7 +35,7 @@
         {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
-        <input type="hidden" name="num_vals" value="{{ n_samples }}">
+        <input type="hidden" name="n_samples" value="{{ n_samples }}">
         <input type="hidden" name="maf" value="{{ maf }}">
         <input type="hidden" name="use_loco" value="{{ use_loco }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
@@ -435,7 +435,7 @@
                             'score_type', 'suggestive', 'significant', 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', 'num_bootstrap', 'bootCheck', 'bootstrap_results',
                             'LRSCheck', 'covariates', 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'control_marker_db', 'do_control', 'genofile', 
                             'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', 
-                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'num_vals']
+                            'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples']
 
         $('input[name=wanted_inputs]').val(mapping_input_list.join(","));
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 80164a22..131345d3 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -630,7 +630,7 @@ def loading_page():
     logger.info(request.url)
     initial_start_vars = request.form
     start_vars_container = {}
-    num_vals = 0 #ZS: So it can be displayed on loading page
+    n_samples = 0 #ZS: So it can be displayed on loading page
     if 'wanted_inputs' in initial_start_vars:
         wanted = initial_start_vars['wanted_inputs'].split(",")
         start_vars = {}
@@ -638,8 +638,8 @@ def loading_page():
             if key in wanted or key.startswith(('value:')):
                 start_vars[key] = value
 
-        if 'num_vals' in start_vars:
-            num_vals = int(start_vars['num_vals'])
+        if 'n_samples' in start_vars:
+            n_samples = int(start_vars['n_samples'])
         else:
             if 'group' in start_vars:
                 dataset = create_dataset(start_vars['dataset'], group_name = start_vars['group'])
@@ -658,9 +658,9 @@ def loading_page():
             for sample in samples:
                 value = start_vars.get('value:' + sample)
                 if value != "x":
-                    num_vals += 1
+                    n_samples += 1
 
-        start_vars['num_vals'] = num_vals
+        start_vars['n_samples'] = n_samples
         start_vars['wanted_inputs'] = initial_start_vars['wanted_inputs']
 
         start_vars_container['start_vars'] = start_vars
@@ -730,7 +730,7 @@ def mapping_results_page():
         'mapmodel_rqtl_geno',
         'temp_trait',
         'reaper_version',
-        'num_vals',
+        'n_samples',
         'transform'
     )
     start_vars = {}