Made R/qtl metho/model names better and added some javascript to disable wrong combinations of options

4 files changed, 55 insertions, 18 deletions

diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 7ee3ac01..c0d6dc0b 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -187,7 +187,10 @@ class RunMapping(object):
             self.mapping_scale = "morgan"
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
-            self.method = start_vars['mapmethod_rqtl_geno']
+            if 'mapmethod_rqtl_geno' in start_vars:
+                self.method = start_vars['mapmethod_rqtl_geno']
+            else:
+                self.method = "em"
             self.model = start_vars['mapmodel_rqtl_geno']
             #if start_vars['pair_scan'] == "true":
             #    self.pair_scan = True
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 932260de..c7e6be4c 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -199,6 +199,7 @@ class ShowTrait(object):
 
         #ZS: Needed to know whether to display bar chart + get max sample name length in order to set table column width
         self.num_values = 0
+        self.binary = "true" #ZS: So it knows whether to display the Binary R/qtl mapping method, which doesn't work unless all values are 0 or 1
         max_samplename_width = 1
         for group in self.sample_groups:
             for sample in group.sample_list:
@@ -206,6 +207,8 @@ class ShowTrait(object):
                     max_samplename_width = len(sample.name)
                 if sample.display_value != "x":
                     self.num_values += 1
+                    if sample.display_value != 0 or sample.display_value != 1:
+                        self.binary = "false"
 
         sample_column_width = max_samplename_width * 8
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
index 3eb34d03..2ab87d03 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -245,6 +245,28 @@
 
   $("#mapping_method_choice").change(mapping_method_fields);
 
+  $("#mapmodel_rqtl_geno").change(function() {
+    if ($(this).val() == "np"){
+      $("#mapmethod_rqtl_geno").attr('disabled', 'disabled');
+      $("#mapmethod_rqtl_geno").css('background-color', '#CCC');
+      $("#missing_geno").attr('disabled', 'disabled');
+      $("#missing_geno").css('background-color', '#CCC');
+    } else {
+      $("#mapmethod_rqtl_geno").removeAttr('disabled');
+      $("#mapmethod_rqtl_geno").css('background-color', '#FFF');
+      $("#missing_geno").removeAttr('disabled');
+      $("#missing_geno").css('background-color', '#FFF');
+    }
+  });
+
+  $("#mapmethod_rqtl_geno").change(function() {
+    if ($(this).val() == "mr"){
+      $("#missing_geno_div").css('display', 'block');
+    } else {
+      $("#missing_geno_div").css('display', 'none');
+    }
+  });
+
   toggle_enable_disable = function(elem) {
     return $(elem).prop("disabled", !$(elem).prop("disabled"));
   };
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index e79cf1ab..c7fd2612 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -265,31 +265,40 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+                            <label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
-                              <select name="mapmethod_rqtl_geno" class="form-control">
-                                <option value="hk" selected>hk</option>
-                                <option value="em">em</option>
-                                <option value="imp">imp</option>
-                                <option value="ehk">ehk</option>
-                                <option value="mr">mr</option>
-                                <option value="mr-imp">mr-imp</option>
-                                <option value="mr-argmax">mr-argmax</option>
+                              <select id="mapmodel_rqtl_geno" name="mapmodel_rqtl_geno" class="form-control">
+                                <option value="normal">Normal</option>
+                                {% if binary == "true" %}<option value="binary">Binary</option>{% endif %}
+                                <!--<option value="2part">2-part</option>-->
+                                <option value="np">Non-parametric</option>
                               </select>
                             </div>
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" for="mapmodel_rqtl_geno" class="col-xs-3 control-label">Model</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
-                              <select name="mapmodel_rqtl_geno" class="form-control">
-                                <option value="normal">normal</option>
-                                <!--<option value="binary">binary</option>
-                                <option value="2part">2part</option>-->
-                                <option value="np">np</option>
+                            <label style="text-align:right;" for="mapmethod_rqtl_geno" class="col-xs-3 control-label">Method</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                              <select id="mapmethod_rqtl_geno" name="mapmethod_rqtl_geno" class="form-control">
+                                <option value="hk" selected>Haley-Knott</option>
+                                <option value="ehk">Extended Haley-Knott</option>
+                                <option value="mr">Marker Regression</option>
+                                <option value="em">Expectation-Maximization</option>
+                                <option value="imp">Imputation</option>
                               </select>
                             </div>
                         </div>
+                        <div id="missing_geno_div" class="mapping_method_fields form-group" style="display: none;">
+                            <label style="text-align:right;" for="missing_genotypes" class="col-xs-3 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
+                              <select id="missing_genotype" name="missing_genotypes" class="form-control">
+                                <option value="mr">Remove Samples w/o Genotypes</option>
+                                <option value="mr-imp">Single Imputation</option>
+                                <option value="mr-argmax">Imputation w/ Viterbi Algorithm</option>
+                              </select>
+                            </div>
+                        </div>
+
                         <!--
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:left;" class="col-xs-12 control-label">Pair Scan</label>
@@ -306,7 +315,7 @@
                         </div>
                         -->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+                            <label style="text-align:right;" class="col-xs-3 control-label">Manhattan<br>Plot</label>
                             <div style="margin-left:20px;" class="col-xs-6 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_rqtl" value="True">