Added links for markers in mapping results table when genotypes exist in DB

Added more info to trait details for phenotype traits

Changed order of mapping methods

Fixed layout of mapping loading screen to hopefully be centered on different screen sizes

Improved layout of some elements in mapping results page

10 files changed, 184 insertions, 116 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index bcb14451..087b95b4 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -79,6 +79,16 @@ class MarkerRegression(object):
                     self.samples.append(sample)
                     self.vals.append(value)
 
+        #ZS: Check if genotypes exist in the DB in order to create links for markers
+        if "geno_db_exists" in start_vars:
+            self.geno_db_exists = start_vars['geno_db_exists']
+        else:
+          try:
+            geno_dataset = data_set.create_dataset(self.dataset.group.name + "Geno")
+            self.geno_db_exists = "True"
+          except:
+            self.geno_db_exists = "False"
+
         self.mapping_method = start_vars['method']
         if "results_path" in start_vars:
             self.mapping_results_path = start_vars['results_path']
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 93bd9d42..211cf187 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -174,6 +174,8 @@ class MarkerRegression(object):
         if 'genofile_string' in start_vars:
             self.genofile_string = start_vars['genofile_string']
 
+        self.geno_db_exists = start_vars['geno_db_exists']
+
         #Needing for form submission when doing single chr mapping or remapping after changing options
         self.samples = start_vars['samples']
         self.vals = start_vars['vals']
@@ -576,7 +578,7 @@ class MarkerRegression(object):
         self.gifmap = gifmap.__str__()
 
         self.filename= webqtlUtil.genRandStr("Itvl_")
-        intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='jpeg')
+        intCanvas.save(os.path.join(webqtlConfig.GENERATED_IMAGE_DIR, self.filename), format='png')
         intImg=HT.Image('/image/'+self.filename+'.png', border=0, usemap='#WebQTLImageMap')
 
         #Scales plot differently for high resolution
@@ -616,7 +618,7 @@ class MarkerRegression(object):
         else:
             showLocusForm = intImg
 
-        if self.permChecked and self.nperm > 0 and not self.multipleInterval and 0 < self.nperm:
+        if (self.permChecked and self.nperm > 0) and not (self.multipleInterval and 0 < self.nperm):
             self.perm_filename = self.drawPermutationHistogram()
             #perm_text_file = self.permutationTextFile()
 
@@ -1200,8 +1202,10 @@ class MarkerRegression(object):
         if self.controlLocus and self.doControl != "false":
             string2 = 'Using %s as control' % self.controlLocus
         else:
-            if self.mapping_method == "gemma":
+            if self.mapping_method == "gemma" or self.mapping_method == "gemma_bimbam":
                 string2 = 'Using GEMMA mapping method with no control for other QTLs.'
+            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":
                 string2 = 'Using PLINK mapping method with no control for other QTLs.'
             else:
@@ -1963,6 +1967,8 @@ class MarkerRegression(object):
 
             if self.permChecked and self.nperm > 0 and not self.multipleInterval:
                 LRS_LOD_Max = max(self.significant, LRS_LOD_Max)
+            else:
+                LRS_LOD_Max = 1.15*LRS_LOD_Max
 
             #genotype trait will give infinite LRS
             LRS_LOD_Max = min(LRS_LOD_Max, webqtlConfig.MAXLRS)
@@ -2164,10 +2170,7 @@ class MarkerRegression(object):
                 #    Yc = yZero - qtlresult['lrs_value']*LRSHeightThresh/LRS_LOD_Max
 
                 if self.manhattan_plot == True:
-                    if previous_chr_as_int % 2 == 1:
-                        point_color = pid.grey
-                    else:
-                        point_color = pid.black
+                    point_color = pid.black
                     canvas.drawString("5", Xc-canvas.stringWidth("5",font=symbolFont)/2+1,Yc+2,color=point_color, font=symbolFont)
                 else:
                     LRSCoordXY.append((Xc, Yc))
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 8de85a86..b7ebb9ed 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2974,6 +2974,20 @@
                ]
             ]
          },
+         "BXD-Harvested": {
+            "Liver mRNA": [
+               [
+                  "843",
+                  "UTHSC-BXD-Harv_Liv-0118",
+                  "UTHSC BXD Harvested Liver RNA-Seq (Jan18) Log2 **"
+               ],
+               [
+                  "842",
+                  "UTHSC-BXD-Liv-0917",
+                  "UTHSC BXD Liver Affy Clariom S GeneLevel Main (Sep17) RMA **"
+               ]
+            ]
+         },
          "BXD300": {
             "Genotypes": [
                [
@@ -3864,6 +3878,10 @@
             "BXD Bone"
          ],
          [
+            "BXD-Harvested",
+            "BXD NIA Longevity Study"
+         ],
+         [
             "BXD300",
             "BXD300"
          ],
@@ -5007,6 +5025,12 @@
                "Phenotypes"
             ]
          ],
+         "BXD-Harvested": [
+            [
+               "Liver mRNA",
+               "Liver mRNA"
+            ]
+         ],
          "BXD300": [
             [
                "Phenotypes",
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 2f1d836a..4d98f5d8 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 +245,7 @@
       //$("#static_progress_bar_container").modal();
       url = "/loading";
       $('input[name=method]').val("gemma_bimbam");
+      $('input[name=num_perm]').val(0);
       $('input[name=genofile]').val($('#genofile_gemma').val());
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
       form_data = $('#trait_data_form').serialize();
diff --git a/wqflask/wqflask/templates/loading.html b/wqflask/wqflask/templates/loading.html
index cede0e86..46136ddb 100644
--- a/wqflask/wqflask/templates/loading.html
+++ b/wqflask/wqflask/templates/loading.html
@@ -1,20 +1,20 @@
 <title>Loading Mapping Results</title>
 <link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/bootstrap.css" />
-<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/non-responsive.css" />
-<link REL="stylesheet" TYPE="text/css" href="/static/packages/bootstrap/css/docs.css" />
-<link rel="stylesheet" type="text/css" href="/static/packages/colorbox/example4/colorbox.css"  />
-<link rel="stylesheet" type="text/css" href="/static/new/css/main.css"  />
 <form method="post" action="/marker_regression" name="loading_form" id="loading_form" class="form-horizontal">
   {% for key, value in start_vars.iteritems() %}
   <input type="hidden" name="{{ key }}" value="{{ value }}">
   {% endfor %}
   <div class="container">
-    <div class="row">
-      <div style="margin-left: 46%; margin-right: 50%; min-height: 100vh; display: flex; align-items: center;">
-        <h1>Loading&nbsp;Mapping&nbsp;Results...</h1>
+    <div>
+      <div style="min-height: 80vh; display: flex; align-items: center;">
+        <div class="center-block" style="margin-left: 38%; margin-right: 38%; position: absolute; height:50px; width:24%; top:40%;">
+          <h1>Loading&nbsp;Mapping&nbsp;Results...</h1>
+        </div>
       </div>
-      <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
-        <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+      <div style="min-height: 80vh; display: flex; align-items: center;">
+        <div class="progress center-block" style="margin-left: 25%; margin-right: 25%; position: absolute; height:50px; width:50%; top:50%;">
+          <div class="progress-bar progress-bar-striped active" role="progressbar" aria-valuenow="100" aria-valuemin="0" aria-valuemax="100" style="width:100%;"></div>
+        </div>
       </div>
     </div>
   </div>
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index d13c68cd..08a934a6 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -15,6 +15,7 @@
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
         <input type="hidden" name="genofile" value="{{ genofile_string }}">
+        <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}">
         <input type="hidden" name="results_path" value="{{ mapping_results_path }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
         {% for sample in samples %}
@@ -154,7 +155,7 @@
             <div class="tab-pane active" id="gn1_map">
               <div class="qtlcharts">
                   {{ gifmap|safe }}
-                  <img src="/generated/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+                  <img src="/generated/{{ filename }}.png" usemap="#WebQTLImageMap">
                   {% if additiveChecked|upper == "ON" %}
                   <br>
                   <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span>
@@ -180,10 +181,10 @@
 
         </form>
         {% if selectedChr == -1 %}
-        <div style="width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};">
-          <h2>Results</h2>
-          <div id="table_container">
-          <table id="qtl_results" class="table table-hover table-striped nowrap">
+        <div class="container" style="padding-left: 30px; width:{% if 'additive' in trimmed_markers[0] %}45%{% else %}35%{% endif %};">
+          <h2>Mapping Statistics</h2>
+          <div id="table_container" style="border-style: solid; border-width: 1px; border-color: black;">
+          <table id="trait_table" class="table table-hover table-striped nowrap">
             <thead>
               <tr>
                 <th></th>
@@ -194,7 +195,7 @@
                 {% if plotScale != "physic" %}
                 <th>cM</th>
                 {% else %}
-                <th>Mb</th>
+                <th align="right">Mb</th>
                 {% endif %}
                 {% if 'additive' in trimmed_markers[0] %}
                 <th>Add Eff</th>
@@ -209,11 +210,11 @@
               <tr>
                 <td align="center" style="padding-right: 0px;">
                   <input type="checkbox" name="selectCheck"
-                         class="checkbox edit_sample_checkbox"
-                         value="{{ marker.name }}" checked="checked">
+                         class="checkbox trait_checkbox"
+                         value="{{ marker.name }}">
                 </td>
                 <td align="right">{{ loop.index }}</td>
-                <td>{{ marker.name }}</td>
+                <td>{% if geno_db_exists == "True" %}<a href="/show_trait?trait_id={{ marker.name }}&dataset={{ dataset.group.name }}Geno">{{ marker.name }}</a>{% else %}{{ marker.name }}{% endif %}</td>
                 {% if LRS_LOD == "LOD" or LRS_LOD == "-log(p)" %}
                 {% if 'lod_score' in marker %}
                 <td align="right">{{ '%0.2f' | format(marker.lod_score|float) }}</td>
@@ -294,6 +295,7 @@
     </script>
     {% endif %}
 
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script>
     {% if mapping_method != "gemma" and mapping_method != "plink" %}
     <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> 
@@ -304,7 +306,7 @@
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
             console.time("Creating table");
-            $('#qtl_results').DataTable( {
+            $('#trait_table').DataTable( {
                 {% if mapping_method != "reaper" %}
                 "columns": [
                     { "type": "natural", "width": "5%" },
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index a291baf3..dd4325e7 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -28,7 +28,9 @@
 -->
     <div class="container">
         <h2>Trait Data and Analysis for <b>{{ this_trait.name }}</b></h2>
+        {% if this_trait.dataset.type != 'Publish' %}
         <h3>{{ this_trait.description_fmt }}</h3>
+        {% endif %}
     </div>
 
     <form method="post" action="/corr_compute" target="_blank" name="trait_page" id="trait_data_form"
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 2a62733e..1e6d41c2 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -8,6 +8,22 @@
         <td>Tissue</td>
         <td>{{ this_trait.dataset.tissue }}</td>
     </tr>
+    <tr>
+        <td>Phenotype</td>
+        <td><div style="width:40%;">{{ this_trait.description_fmt }}</div></td>
+    </tr>
+    <tr>
+        <td>Authors</td>
+        <td><div style="width:40%;">{{ this_trait.authors }}</div></td>
+    </tr>
+    <tr>
+        <td>Title</td>
+        <td><div style="width:40%;">{{ this_trait.title }}</div></td>
+    </tr>
+    <tr>
+        <td>Journal</td>
+        <td>{{ this_trait.journal }} (<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">{{ this_trait.year }}</a>)</td>
+    </tr>
     {% endif %}
     {% if this_trait.dataset.type == 'ProbeSet' %}
     {% if this_trait.symbol != None %}
@@ -50,22 +66,29 @@
         </td>
     </tr>
     {% endif %}
+    {% if this_trait.pubmed_id or this_trait.geneid or this_trait.omim or this_trait.symbol %}
+    {% if this_trait.dataset.type != 'Publish' %}
     <tr>
         <td>Resource Links</td>
         <td>
-            {% if this_trait.geneid != None %}
+            {% if this_trait.pubmed_id %}
+            <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ this_trait.pubmed_id }}&dop=Abstract" title="PubMed">
+                PubMed
+            </a>
+            {% endif %}
+            {% if this_trait.geneid %}
             <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids={{ this_trait.geneid }}" title="Info from NCBI Entrez Gene">
                 NCBI
             </a>
             &nbsp;&nbsp;
             {% endif %}
-            {% if this_trait.omim != None %}
+            {% if this_trait.omim %}
             <a href="http://www.ncbi.nlm.nih.gov/omim/{{ this_trait.omim }}" title="Summary from On Mendelion Inheritance in Man">
                 OMIM
             </a>
             &nbsp;&nbsp;
             {% endif %}
-            {% if this_trait.symbol != None %}
+            {% if this_trait.symbol %}
             <a href="http://www.genotation.org/Getd2g.pl?gene_list={{ this_trait.symbol }}" title="Related descriptive, genomic, clinical, functional and drug-therapy information">
                 Genotation
             </a>
@@ -77,6 +100,8 @@
         {% endif %}
         </td>
     </tr>
+    {% endif %}
+    {% endif %}
 </table>
 
 <div style="margin-bottom:15px;" class="btn-toolbar">
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 77f78415..dcec2b9e 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -6,16 +6,16 @@
             <ul class="nav nav-pills">
                 {% if dataset.group.mapping_id == "1" %}
                 <li class="active">
-                    <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
+                    <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
                 <li>
-                    <a href="#pylmm" data-toggle="tab">pyLMM</a>
+                    <a href="#interval_mapping" data-toggle="tab">Interval Mapping</a>
                 </li>
                 <li>
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
                 <li>
-                    <a href="#gemma" data-toggle="tab">GEMMA</a>
+                    <a href="#pylmm" data-toggle="tab">pyLMM</a>
                 </li>
                 {% endif %}
                 {% for mapping_method in dataset.group.mapping_names %}
@@ -37,7 +37,60 @@
             <div class="tab-content">
                 {# if use_pylmm_rqtl and not use_plink_gemma and dataset.group.species != "human" #}
                 {% if dataset.group.mapping_id == "1" %}
-                <div class="tab-pane active" id="interval_mapping">
+                <div class="tab-pane active" id="gemma">
+                    <div style="padding-top: 10px;" class="form-horizontal">
+                        {% if genofiles and genofiles|length>0 %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
+                            <div style="margin-left: 20px;" class="col-xs-8 controls">
+                                <select id="genofile_gemma" class="form-control">
+                                    {% for item in genofiles %}
+                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
+                        {% endif %}
+                        <div class="mapping_method_fields form-group">
+                            <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
+                            <div style="margin-left: 20px;" class="col-xs-3 controls">
+                                <input name="maf_gemma" value="0.01" type="text" class="form-control">
+                            </div>
+                        </div>
+                        <div class="mapping_method_fields form-group">
+                            <label class="col-xs-4 control-label">Use LOCO</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="True">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="use_loco" value="False" checked="">
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                    </div>
+                    <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
+                        <div class="mapping_method_fields form-group">
+                            <button type="button" id="select_covariates" class="btn btn-default">
+                                Select Covariates
+                            </button>
+                            <button type="button" id="remove_covariates" class="btn btn-default">
+                                Remove Covariates
+                            </button>
+                        </div>
+                    </div>
+
+                    <div class="form-group">
+                        <div class="col-xs-4 controls">
+                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
+                                Compute
+                            </button>
+                        </div>
+                    </div>
+                </div>
+                <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
@@ -131,62 +184,6 @@
                         <!--<div id="alert_placeholder"></div>-->
                     </div>
                 </div>
-                <div class="tab-pane" id="pylmm">
-                    <div style="margin-top: 20px" class="form-horizontal">
-                        {% if genofiles and genofiles|length>0 %}
-                        <div class="mapping_method_fields form-group">
-                            <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
-                            <div style="margin-left: 20px;" class="col-xs-8 controls">
-                                <select id="genofile_pylmm" class="form-control">
-                                    {% for item in genofiles %}
-                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
-                                    {% endfor %}
-                                </select>
-                            </div>
-                        </div>
-                        {% endif %}
-<!--
-                        <div class="mapping_method_fields form-group">
-                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
-                                {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
-                                <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
-                                {% else %}
-                                <input name="control_pylmm" value="" type="text" />
-                                {% endif %}
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_pylmm" value="true">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="do_control_pylmm" value="false" checked="">
-                                    No
-                                </label>
-                            </div>
-                        </div>
-                        <div class="mapping_method_fields form-group">
-                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
-                            <div class="col-xs-12 controls">
-                                <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_pylmm" value="True">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
-                                    No
-                               </label>
-                            </div>
-                        </div>
--->
-                        <div class="form-group">
-                            <div style="padding-left:15px;" class="controls">
-                                <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
-                                    <i class="icon-ok-circle icon-white"></i> Compute
-                                </button>
-                            </div>
-                        </div>
-                    </div>
-                </div>
                 <div class="tab-pane" id="rqtl_geno">
 
                     <div style="margin-top: 20px" class="form-horizontal">
@@ -294,13 +291,13 @@
                         </div>
                     </div>
                 </div>
-                <div class="tab-pane" id="gemma">
-                    <div style="padding-top: 10px;" class="form-horizontal">
+                <div class="tab-pane" id="pylmm">
+                    <div style="margin-top: 20px" class="form-horizontal">
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
                             <label for="genofiles" class="col-xs-3 control-label">Genotypes</label>
                             <div style="margin-left: 20px;" class="col-xs-8 controls">
-                                <select id="genofile_gemma" class="form-control">
+                                <select id="genofile_pylmm" class="form-control">
                                     {% for item in genofiles %}
                                     <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                     {% endfor %}
@@ -308,42 +305,45 @@
                             </div>
                         </div>
                         {% endif %}
+<!--
                         <div class="mapping_method_fields form-group">
-                            <label for="maf_gemma" class="col-xs-5 control-label">Minor allele threshold</label>
-                            <div style="margin-left: 20px;" class="col-xs-3 controls">
-                                <input name="maf_gemma" value="0.01" type="text" class="form-control">
+                            <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
+                                <input name="control_pylmm" value="{{ nearest_marker }}" type="text" />
+                                {% else %}
+                                <input name="control_pylmm" value="" type="text" />
+                                {% endif %}
+                                <label class="radio-inline">
+                                    <input type="radio" name="do_control_pylmm" value="true">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="do_control_pylmm" value="false" checked="">
+                                    No
+                                </label>
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-4 control-label">Use LOCO</label>
-                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+                            <div class="col-xs-12 controls">
                                 <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="True">
+                                    <input type="radio" name="manhattan_plot_pylmm" value="True">
                                     Yes
                                 </label>
                                 <label class="radio-inline">
-                                    <input type="radio" name="use_loco" value="False" checked="">
+                                    <input type="radio" name="manhattan_plot_pylmm" value="False" checked="">
                                     No
                                </label>
                             </div>
                         </div>
-                    </div>
-                    <div style="padding-top: 5px; padding-bottom: 5px; padding-left: 20px;" class="form-horizontal">
-                        <div class="mapping_method_fields form-group">
-                            <button type="button" id="select_covariates" class="btn btn-default">
-                                Select Covariates
-                            </button>
-                            <button type="button" id="remove_covariates" class="btn btn-default">
-                                Remove Covariates
-                            </button>
-                        </div>
-                    </div>
-
-                    <div class="form-group">
-                        <div class="col-xs-4 controls">
-                            <button id="gemma_bimbam_compute" class="btn submit_special btn-success" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
+-->
+                        <div class="form-group">
+                            <div style="padding-left:15px;" class="controls">
+                                <button id="pylmm_compute" class="btn submit_special btn-success" title="Compute Marker Regression">
+                                    <i class="icon-ok-circle icon-white"></i> Compute
+                                </button>
+                            </div>
                         </div>
                     </div>
                 </div>
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 68e779a1..d8f5616d 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -557,6 +557,7 @@ def marker_regression_page():
     wanted = (
         'trait_id',
         'dataset',
+        'geno_db_exists',
         'method',
         'mapping_results_path',
         'trimmed_markers',