Changed appearance of mapping and correlation options on trait page

Fixed issue where changed sample values were not passed to qtlreaper mapping ("Interval Mapping")

Loading factors and their plot are hidden in situations where there's some error with calculating principal components

Added GEMMA description and changed order of descriptions for mapping options on trait page

8 files changed, 125 insertions, 113 deletions

diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index b34beb7b..077386a3 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -173,9 +173,12 @@ class CorrelationMatrix(object):
             for sample in self.all_sample_list:
                 groups.append(1)
 
-            pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
-
-            self.loadings_array = self.process_loadings()
+            try:
+                self.pca_works = "True"
+                pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
+                self.loadings_array = self.process_loadings()
+            except:
+                self.pca_works = "False"
 
             self.js_data = dict(traits = [trait.name for trait in self.traits],
                                 groups = groups,
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 087b95b4..db4f8f46 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -228,6 +228,7 @@ class MarkerRegression(object):
             results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
                                                                                                                                                         self.dataset,
                                                                                                                                                         self.samples,
+                                                                                                                                                        self.vals,
                                                                                                                                                         self.json_data,
                                                                                                                                                         self.num_perm,
                                                                                                                                                         self.bootCheck,
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 211cf187..66884b0c 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -1204,6 +1204,8 @@ class MarkerRegression(object):
         else:
             if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
                 string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+                if self.covariates != "":
+                    string3 = 'Using following traits as covariates: ' + self.covariates
             elif self.mapping_method == "rqtl_plink" or self.mapping_method == "rqtl_geno":
                 string2 = 'Using R/qtl mapping method with no control for other QTLs.'
             elif self.mapping_method == "plink":
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index 50228b5e..6b58190f 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -1,17 +1,20 @@
-def gen_reaper_results(this_trait, dataset, samples_before, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
+import utility.logger
+logger = utility.logger.getLogger(__name__ )
+
+def gen_reaper_results(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
     genotype = dataset.group.read_genotype_file()
 
     if manhattan_plot != True:
         genotype = genotype.addinterval()
 
-    samples, values, variances, sample_aliases = this_trait.export_informative()
-
     trimmed_samples = []
     trimmed_values = []
-    for i in range(0, len(samples)):
-        if this_trait.data[samples[i]].name in samples_before:
-            trimmed_samples.append(samples[i])
-            trimmed_values.append(values[i])
+    for i in range(0, len(samples_before)):
+        try:
+            trimmed_values.append(float(trait_vals[i]))
+            trimmed_samples.append(samples_before[i])
+        except:
+            pass
 
     perm_output = []
     bootstrap_results = []
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index ab793d58..d27788a8 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -61,6 +61,7 @@
 <br>
 <button class="btn btn-default" id="short_labels">Short Labels</button>
 <button class="btn btn-default" id="long_labels">Long Labels</button>
+{% if pca_works == "True" %}
 <br>
 <br>
 <h2>Factor Loadings Plot</h2>
@@ -93,7 +94,7 @@
   </tbody>
 </table>
 </div>
-
+{% endif %}
 {% endblock %}
 
 {% block js %}
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index c5f815ce..ef233333 100644
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -1,9 +1,10 @@
 <div>
+  <div class="col-xs-7">
     <div style="padding: 20px" class="form-horizontal">
         
         <div class="form-group">
-            <label for="corr_type" class="col-xs-1 control-label">Method</label>
-            <div class="col-xs-2 controls">
+            <label for="corr_type" class="col-xs-2 control-label">Method</label>
+            <div class="col-xs-3 controls">
                 <select name="corr_type" class="form-control">
                     <option value="sample">Sample r</option>
                     <option value="lit">Literature r</option>
@@ -13,8 +14,8 @@
         </div>
         
         <div class="form-group">
-            <label for="corr_dataset" class="col-xs-1 control-label">Database</label>
-            <div class="col-xs-6 controls">
+            <label for="corr_dataset" class="col-xs-2 control-label">Database</label>
+            <div class="col-xs-10 controls">
                 <select name="corr_dataset" class="form-control">
                     {% for tissue in corr_tools.dataset_menu %}
                         {% if tissue.tissue %}
@@ -37,8 +38,8 @@
         </div>
         
         <div class="form-group">
-            <label for="corr_return_results" class="col-xs-1 control-label">Return</label>
-            <div class="col-xs-2 controls">
+            <label for="corr_return_results" class="col-xs-2 control-label">Return</label>
+            <div class="col-xs-3 controls">
                 <select name="corr_return_results" class="form-control">
                     {% for return_result in corr_tools.return_results_menu %}
                         <option value="{{ return_result }}" 
@@ -53,8 +54,8 @@
         </div>
         
         <div class="form-group">
-            <label for="corr_samples_group" class="col-xs-1 control-label">Samples</label>
-            <div class="col-xs-2 controls">
+            <label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
+            <div class="col-xs-3 controls">
                 <select name="corr_samples_group" class="form-control">
                     {% for group, pretty_group in sample_group_types.items() %}
                         <option value="{{ group }}">{{ pretty_group }}</option>
@@ -64,8 +65,8 @@
         </div>
             
         <div id="corr_sample_method" class="form-group">
-            <label for="corr_sample_method" class="col-xs-1 control-label">Type</label>
-            <div class="col-xs-2 controls">
+            <label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
+            <div class="col-xs-3 controls">
                 <select name="corr_sample_method" class="form-control">
                     <option value="pearson">Pearson</option>
                     <option value="spearman">Spearman Rank</option>
@@ -73,14 +74,14 @@
             </div>
         </div>
         <div class="form-group">
-            <label class="col-xs-1 control-label">Min Expr</label>
-            <div class="col-xs-2 controls">
+            <label class="col-xs-2 control-label">Min Expr</label>
+            <div class="col-xs-3 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">Location</label>
-            <div class="col-xs-4 controls">
+            <label class="col-xs-2 control-label">Location</label>
+            <div class="col-xs-5 controls">
                 <span>
                 Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">&nbsp;&nbsp;&nbsp;
                 Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> &nbsp;to&nbsp; <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
@@ -89,8 +90,8 @@
             </div>
         </div>
         <div class="form-group">
-            <label class="col-xs-1 control-label">Range</label>
-            <div class="col-xs-4 controls">
+            <label class="col-xs-2 control-label">Range</label>
+            <div class="col-xs-5 controls">
                 <input name="p_range_lower" value="" type="hidden">
                 <input name="p_range_upper" value="" type="hidden">
                 <span style="display: inline;">
@@ -103,48 +104,45 @@
         </div>
         
         <div class="form-group">
-            <label for="corr_sample_method" class="col-xs-1 control-label"></label>
-            <div class="col-xs-4 controls">
+            <label for="corr_sample_method" class="col-xs-2 control-label"></label>
+            <div class="col-xs-3 controls">
                 <button class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation">
                     <i class="icon-ok-circle icon-white"></i> Compute
                 </button>
             </div>
         </div>
-
-        <div class="form-group">
-            <label for="descriptions" class="col-xs-1 control-label"></label>
-            <div class="col-xs-6 controls">
-            <span id="sample_r_desc" class="correlation_desc fs12">
-                The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
-                is computed
-                between trait data and any
-                other traits in the sample database selected above. Use
-                <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
-                Rank</a>
-                when the sample size is small (&lt;20) or when there are influential outliers.
-            </span>
-            <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
-                The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
-                (Lit r) between
-                this gene and all other genes is computed<br>
-                using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
-                Semantic Gene Organizer</a>
-                and human, rat, and mouse data from PubMed.
-                Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
-                <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
-            </span>
-            <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
-                The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
-                (Tissue r)
-                estimates the similarity of expression of two genes
-                or transcripts across different cells, tissues, or organs
-                (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
-                Tissue correlations
-                are generated by analyzing expression in multiple samples usually taken from single cases.<br>
-                <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
-                computed for all pairs of genes using data from mouse samples.<br>
-            </span>
-            </div>
-        </div>
     </div>
+  </div>
+  <div class="col-xs-5">
+    <span id="sample_r_desc" class="correlation_desc fs12">
+        The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
+        is computed
+        between trait data and any
+        other traits in the sample database selected above. Use
+        <a href="http://www.genenetwork.org/glossary.html#Correlations">Spearman
+        Rank</a>
+        when the sample size is small (&lt;20) or when there are influential outliers.
+    </span>
+    <span id="lit_r_desc" style="display: none;" class="correlation_desc fs12">
+        The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
+        (Lit r) between
+        this gene and all other genes is computed<br>
+        using the <a href="https://grits.eecs.utk.edu/sgo/sgo.html">
+        Semantic Gene Organizer</a>
+        and human, rat, and mouse data from PubMed.
+        Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
+        <a href="http://genenetwork.org/glossary.html#Literature">More on using Lit r</a>
+    </span>
+    <span id="tissue_r_desc" style="display: none;" class="correlation_desc fs12">
+        The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
+        (Tissue r)
+        estimates the similarity of expression of two genes
+        or transcripts across different cells, tissues, or organs
+        (<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
+        Tissue correlations
+        are generated by analyzing expression in multiple samples usually taken from single cases.<br>
+        <strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
+        computed for all pairs of genes using data from mouse samples.<br>
+    </span>
+  </div>
 </div>
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index ab2e2aae..03590c2c 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -1,5 +1,5 @@
 <div>
-    {% if (use_pylmm_rqtl and dataset.group.species != "human") or use_plink_gemma %}
+    {% if dataset.group.mapping_names|length > 0 %}
     <div class="col-xs-5">
         <div class="tabbable"> <!-- Only required for left/right tabs -->
 
@@ -41,7 +41,7 @@
                     <div style="padding-top: 20px;" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label for="genofiles" style="text-align: left;" class="col-xs-2 control-label">Genotypes</label>
+                            <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_gemma" class="form-control">
                                     {% for item in genofiles %}
@@ -52,20 +52,20 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" style="text-align: left;" class="col-xs-2 control-label">MAF</label>
-                            <div style="margin-left:20px;" class="col-xs-3 controls">
+                            <label for="maf_gemma" style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+                            <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" class="col-xs-2 control-label">Use LOCO</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label style="text-align: right;" class="col-xs-3 control-label">Use LOCO</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
                                 <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="True">
+                                    <input type="radio" name="use_loco" value="True" checked="">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="False" checked="">
+                                    <input type="radio" name="use_loco" value="False">
                                     No
                                </label>
                             </div>
@@ -75,7 +75,7 @@
                     <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
                     -->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" class="col-xs-2 control-label">Covariates</label>
+                            <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
                               {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
                               No collections available. Please add traits to a collection to use them as covariates.
@@ -86,13 +86,13 @@
                                 <button type="button" id="select_covariates" class="btn btn-default">Select</button>
                                 <button type="button" id="remove_covariates" class="btn btn-default">Remove</button>
                               </div>
-                              <textarea rows="2" cols="40" readonly placeholder="No covariates selected" class="selected_covariates"></textarea>
+                              <textarea rows="3" cols="20" readonly placeholder="No covariates selected" style="overflow-y: scroll; resize: none;" class="selected_covariates"></textarea>
                               {% endif %}
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                          <label class="col-xs-2 control-label"></label>
-                          <div style="margin-left:20px;" class="col-xs-4">
+                          <label class="col-xs-3 control-label"></label>
+                          <div style="margin-left:20px;" class="col-xs-6">
                             <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
@@ -116,7 +116,7 @@
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="genofiles" class="col-xs-2 control-label">Genotypes</label>
+                            <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_reaper" class="form-control">
                                     {% for item in genofiles %}
@@ -127,20 +127,20 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+                            <label style="text-align: right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="num_perm_reaper" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="mapping_bootstraps" class="col-xs-2 control-label">Bootstraps</label>
+                            <label style="text-align: right;" for="mapping_bootstraps" class="col-xs-3 control-label">Bootstraps</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="num_bootstrap" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label style="text-align: right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
                                 {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
                                 <input name="control_reaper" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
                                 {% else %}
@@ -184,8 +184,8 @@
 
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-2 control-label">Marker<br>Regression</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label style="text-align: right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_reaper" value="True">
                                     Yes
@@ -197,8 +197,8 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-2 control-label"></label>
-                            <div style="margin-left:20px;" class="col-xs-4">
+                            <label class="col-xs-3 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-6">
                               <button id="interval_mapping_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
                                   Compute
                               </button>
@@ -212,7 +212,7 @@
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="genofiles" class="col-xs-2 control-label">Genotypes</label>
+                            <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <select id="genofile_rqtl_geno" class="form-control">
                                     {% for item in genofiles %}
@@ -223,14 +223,14 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+                            <label style="text-align:right;" for="mapping_permutations" class="col-xs-3 control-label">Permutations</label>
                             <div style="margin-left:20px;" class="col-xs-4 controls">
                                 <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label style="text-align:right;" for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
                                 {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
                                 <input name="control_rqtl_geno" value="{{ nearest_marker }}" type="text" style="width: 160px;" class="form-control" />
                                 {% else %}
@@ -248,7 +248,7 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" for="mapmethod_rqtl_geno" class="col-xs-2 control-label">Method</label>
+                            <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-4 controls">
                               <select name="mapmethod_rqtl_geno" class="form-control">
                                 <option value="em">em</option>
@@ -263,7 +263,7 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" for="mapmodel_rqtl_geno" class="col-xs-2 control-label">Model</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="mapmodel_rqtl_geno" class="form-control">
                                 <option value="normal">normal</option>
@@ -289,8 +289,8 @@
                         </div>
                         -->
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-2 control-label">Marker<br>Regression</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">
+                            <label style="text-align:right;" class="col-xs-3 control-label">Marker<br>Regression</label>
+                            <div style="margin-left:20px;" class="col-xs-6 controls">
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_rqtl" value="True">
                                     Yes
@@ -303,8 +303,8 @@
                         </div>
 
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-2 control-label"></label>
-                            <div style="margin-left:20px;" class="col-xs-4">
+                            <label class="col-xs-3 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-6">
                               <button id="rqtl_geno_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
                                   Compute
                               </button>
@@ -316,7 +316,7 @@
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-2 control-label">Genotypes</label>
+                            <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <select id="genofile_pylmm" class="form-control">
                                     {% for item in genofiles %}
@@ -327,8 +327,8 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-2 control-label"></label>
-                            <div style="margin-left:20px;" class="col-xs-4">
+                            <label class="col-xs-3 control-label"></label>
+                            <div style="margin-left:20px;" class="col-xs-6">
                               <button id="pylmm_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Interval Mapping">
                                   Compute
                               </button>
@@ -343,8 +343,8 @@
                     <div style="padding-top: 10px;" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-4 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
+                            <label style="text-align:right;" class="col-xs-3 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <select id="genofile_gemma" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
@@ -354,13 +354,13 @@
                         </div>
                         {% endif %}
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-2 control-label">MAF</label>
+                            <label style="text-align:right;" class="col-xs-3 control-label">MAF</label>
                             <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <input name="maf_gemma" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label style="text-align: left;" class="col-xs-2 control-label">Covariates</label>
+                            <label style="text-align: right;" class="col-xs-3 control-label">Covariates</label>
                             <div style="margin-left:20px;" class="col-xs-7">
                               {% if g.user_session.user_ob and (g.user_session.user_ob.display_num_collections() == "") %}
                               No collections available. Please add traits to a collection to use them as covariates.
@@ -376,8 +376,8 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                          <label class="col-xs-2 control-label"></label>
-                          <div style="margin-left:20px;" class="col-xs-4">
+                          <label class="col-xs-3 control-label"></label>
+                          <div style="margin-left:20px;" class="col-xs-6">
                             <button id="gemma_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
@@ -389,16 +389,16 @@
                 <div class="tab-pane" id="plink">
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_plink" class="col-xs-3 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-3 controls">
+                            <label style="text-align: right;" class="col-xs-3 control-label">MAF</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 <input name="maf_plink" value="0.01" type="text" class="form-control">
                             </div>
                         </div>
                     </div>
 
                     <div class="form-group">
-                        <label for="plink_compute" class="col-xs-1 control-label"></label>
-                        <div style="margin-left:20px;" class="col-xs-4 controls">
+                        <label style="text-align: right;" class="col-xs-3 control-label"></label>
+                        <div style="margin-left:20px;" class="col-xs-6 controls">
                             <button id="plink_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
                                 Compute
                             </button>
@@ -413,22 +413,26 @@
     <div class="col-xs-5">
         {% if dataset.group.mapping_id == "1" %}
         <dl>
+             <dt>GEMMA</dt>
+             <dd>GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).</dd>
              <dt>Interval Mapping</dt>
              <dd>Interval mapping is a process in which the statistical significance of a hypothetical QTL is evaluated at regular points across a chromosome, even in the absence of explicit genotype data at those points.</dd>
-             <dt>pyLMM</dt>
-             <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
              <dt>R/qtl</dt>
              <dd>R/qtl is an extensible, interactive environment for mapping quantitative trait loci (QTL) in experimental crosses.</dd>
+             <dt>pyLMM</dt>
+             <dd>pyLMM is a fast and lightweight linear mixed-model (LMM) solver for use in genome-wide association studies (GWAS).</dd>
         </dl>
         {% else %}
         <dl>
+            {% if mapping_method == "GEMMA" %}
             <dt>GEMMA</dt>
             <dd>
                 GEMMA is software implementing the Genome-wide Efficient Mixed Model Association algorithm for a standard linear mixed model for genome-wide association studies (GWAS).<br>
-                Note: There currently exists an issue where GEMMA can't be run on traits from the same group simultaneously. If you receive an error, please wait a few minutes and try again.
             </dd>
+            {% elif mapping_method == "PLINK" %}
             <dt>PLINK</dt>
             <dd>PLINK is a free, open-source whole genome association analysis toolset.</dd>
+            {% endif %}
         </dl>
         {% endif %}
     </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 187b60dc..17a2d762 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -582,7 +582,7 @@ def marker_regression_page():
         'control_marker',
         'control_marker_db',
         'do_control',
-        'genofile',
+        'genofile_string',
         'pair_scan',
         'startMb',
         'endMb',