Added option to select chromosome from trait page when mapping

Put transform/blocking tools into their own tab (still need to change formatting of tab's contents)

Improved appearance of search result page table (still need to change a few other tables)

Fixed issue that caused parent/f1 strains to not be blocked correctly when using "block by index" tool

Basic Stats figures now load when the user clicks the tab, to improve initial page load time

17 files changed, 322 insertions, 146 deletions

diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index ad0eb036..b53f5dda 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -54,8 +54,8 @@ class GenerateKinshipMatrices(object):
     
     
 if __name__=="__main__":
-    Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
-    Bimbam_Directory = """/home/zas1024/genotype_files/genotype/bimbam/"""
+    Geno_Directory = """/export/local/home/zas1024/genotype_files/genotype/"""
+    Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
     GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
     
     #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
\ No newline at end of file
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 789a1691..9579812a 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -24,6 +24,8 @@ import simplejson as json
 
 from pprint import pformat as pf
 
+#from utility.tools import flat_files
+
 class EmptyConfigurations(Exception): pass
 
         
@@ -183,8 +185,8 @@ class ConvertGenoFile(object):
 
 
 if __name__=="__main__":
-    Old_Geno_Directory = """/home/zas1024/genotype_files/genotype/"""
-    New_Geno_Directory = """/home/zas1024/genotype_files/genotype/json/"""
+    Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
+    New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
     #Input_File = """/home/zas1024/gene/genotype_files/genotypes/BXD.geno"""
     #Output_File = """/home/zas1024/gene/wqflask/wqflask/pylmm/data/bxd.snps"""
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 31d47ff2..6d9f07a0 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -63,10 +63,7 @@ class SampleList(object):
                 sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
                 sample.extra_info['css_class'] = "fs12"
 
-            if sample_group_type == 'primary':
-                sample.this_id = "Primary_" + str(counter)
-            else:
-                sample.this_id = "Other_" + str(counter)
+            sample.this_id = str(counter)
 
             #### For extra attribute columns; currently only used by several datasets - Zach
             if self.sample_attribute_values:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 34447853..7d6dd74e 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -153,7 +153,8 @@ class ShowTrait(object):
            hddn['group'] = self.temp_group
            hddn['species'] = self.temp_species
         hddn['use_outliers'] = False
-        hddn['method'] = "pylmm"
+        hddn['method'] = "gemma"
+        hddn['selected_chr'] = -1
         hddn['mapping_display_all'] = True
         hddn['suggestive'] = 0
         hddn['num_perm'] = 0
@@ -182,6 +183,11 @@ class ShowTrait(object):
             self.sample_group_types['samples_primary'] = self.dataset.group.name
         sample_lists = [group.sample_list for group in self.sample_groups]
 
+        #ZS: Get list of chromosomes to select for mapping
+        self.chr_list = [["All", -1]]
+        for i, this_chr in enumerate(self.species.chromosomes.chromosomes):
+            self.chr_list.append([self.species.chromosomes.chromosomes[this_chr].name, i])
+
         self.genofiles = get_genofiles(self.dataset)
 
         self.has_num_cases = has_num_cases(self.this_trait)
diff --git a/wqflask/wqflask/static/new/css/show_trait.css b/wqflask/wqflask/static/new/css/show_trait.css
index aa47d13f..c03b6103 100644
--- a/wqflask/wqflask/static/new/css/show_trait.css
+++ b/wqflask/wqflask/static/new/css/show_trait.css
@@ -27,6 +27,10 @@ table.dataTable thead .sorting_desc {
   background-image: url("../packages/DataTables/images/sort_desc_disabled.png");
 }
 
+table.dataTable thead th {
+  padding: 4px 18px 4px 10px;
+}
+
 table.dataTable tbody td {
   padding: 3px 20px 1px 10px;
 }
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 9c806a7f..72008225 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -1557,6 +1557,42 @@
                ]
             ]
          },
+         "AIL-LGSM-F34-A": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "AIL-LGSM-F34-APublish",
+                  "AIL-LGSM-F34-A Phenotypes"
+               ]
+            ]
+         },
+         "AIL-LGSM-F34-F39-43-GBS": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "AIL-LGSM-F34-F39-43-GBSPublish",
+                  "AIL-LGSM-F34-F39-43-GBS Phenotypes"
+               ]
+            ]
+         },
+         "AIL-LGSM-F34-GBS": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "AIL-LGSM-F34-GBSPublish",
+                  "AIL-LGSM-F34-GBS Phenotypes"
+               ]
+            ]
+         },
+         "AIL-LGSM-F39-43-GBS": {
+            "Phenotypes": [
+               [
+                  "None",
+                  "AIL-LGSM-F39-43-GBSPublish",
+                  "AIL-LGSM-F39-43-GBS Phenotypes"
+               ]
+            ]
+         },
          "AKXD": {
             "Genotypes": [
                [
@@ -2591,6 +2627,11 @@
             ],
             "Liver mRNA": [
                [
+                  "857",
+                  "EPFLMouseLiverCDHFDRMA0818",
+                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
+               ],
+               [
                   "859",
                   "EPFLMouseLiverCDRMA0818",
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
@@ -2621,11 +2662,6 @@
                   "NIA Aging BXD HFD Liver Affy Clariom S Gene Level (Aug18) RMA **"
                ],
                [
-                  "857",
-                  "EPFLMouseLiverCDHFDRMA0818",
-                  "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Aug18) RMA"
-               ],
-               [
                   "430",
                   "EPFLMouseLiverRMA0413",
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
@@ -2641,6 +2677,11 @@
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA"
                ],
                [
+                  "848",
+                  "EPFLMouseLiverHFCEx0413",
+                  "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
+               ],
+               [
                   "433",
                   "EPFLMouseLiverBothExRMA0413",
                   "EPFL/LISP BXD CD+HFD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
@@ -2651,11 +2692,6 @@
                   "EPFL/LISP BXD CD Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
                ],
                [
-                  "848",
-                  "EPFLMouseLiverHFCEx0413",
-                  "EPFL/LISP BXD HFC Liver Affy Mouse Gene 1.0 ST (Apr13) RMA Exon Level"
-               ],
-               [
                   "700",
                   "UTHSC-VGX_MmBXDHepatocytesRMA1014",
                   "UT-VGX Hepatocytes Affy Mouse Gene 1.0 ST Gene Level (Oct14) RMA"
@@ -4002,6 +4038,22 @@
             "AIL Advanced Intercross Line"
          ],
          [
+            "AIL-LGSM-F34-A",
+            "AIL LGSM F34 (Array)"
+         ],
+         [
+            "AIL-LGSM-F34-GBS",
+            "AIL LGSM F34 (GBS)"
+         ],
+         [
+            "AIL-LGSM-F34-F39-43-GBS",
+            "AIL LGSM F34 and F39-43 (GBS)"
+         ],
+         [
+            "AIL-LGSM-F39-43-GBS",
+            "AIL LGSM F39-43 (GBS)"
+         ],
+         [
             "AKXD",
             "AKXD RI Family"
          ],
@@ -4929,6 +4981,30 @@
                "Striatum mRNA"
             ]
          ],
+         "AIL-LGSM-F34-A": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ]
+         ],
+         "AIL-LGSM-F34-F39-43-GBS": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ]
+         ],
+         "AIL-LGSM-F34-GBS": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ]
+         ],
+         "AIL-LGSM-F39-43-GBS": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ]
+         ],
          "AKXD": [
             [
                "Genotypes",
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index df86e764..717d98b9 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -417,16 +417,27 @@
       }
       console.log("towards end:", sample_sets);
       update_stat_values(sample_sets);
-      console.log("redrawing histogram");
-      redraw_histogram();
-      console.log("redrawing bar chart");
-      redraw_bar_chart();
-      console.log("redrawing box plot");
-      redraw_box_plot();
-      console.log("redrawing violin plot");
-      redraw_violin_plot();
-      console.log("redrawing probability plot");
-      return redraw_prob_plot();
+
+      if ($('#histogram').hasClass('js-plotly-plot')){
+        console.log("redrawing histogram");
+        redraw_histogram();
+      }
+      if ($('#bar_chart').hasClass('js-plotly-plot')){
+        console.log("redrawing bar chart");
+        redraw_bar_chart();
+      }
+      if ($('#box_plot').hasClass('js-plotly-plot')){
+        console.log("redrawing box plot");
+        redraw_box_plot();
+      }
+      if ($('#violin_plot').hasClass('js-plotly-plot')){
+        console.log("redrawing violin plot");
+        redraw_violin_plot();
+      }
+      if ($('#prob_plot_div').hasClass('js-plotly-plot')){
+        console.log("redrawing probability plot");
+        return redraw_prob_plot();
+      }
     };
     show_hide_outliers = function() {
       var label;
@@ -853,7 +864,13 @@
         }
       };
       root.bar_layout = layout
-      Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options)
+      $('.bar_chart_tab').click(function() {
+        if ($('#bar_chart').hasClass('js-plotly-plot')){
+          redraw_bar_chart();
+        } else {
+          Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options)
+        }
+      });
     }
 
     if (full_sample_lists.length > 1) {
@@ -957,11 +974,18 @@
         ]
     }
 
-    obj = {
+    box_obj = {
       data: box_data,
       layout: root.box_layout
     }
-    Plotly.newPlot('box_plot', obj, root.modebar_options);
+
+    $('.box_plot_tab').click(function() {
+      if ($('#box_plot').hasClass('js-plotly-plot')){
+        redraw_box_plot();
+      } else {
+        Plotly.newPlot('box_plot', box_obj, root.modebar_options);
+      }
+    });
 
     // Violin Plot
 
@@ -1066,12 +1090,18 @@
         ]
     }
 
-    obj = {
+    violin_obj = {
       data: violin_data,
       layout: root.violin_layout
     }
 
-    Plotly.plot('violin_plot', obj, root.modebar_options)
+    $('.violin_plot_tab').click(function() {
+      if ($('#violin_plot').hasClass('js-plotly-plot')){
+        redraw_violin_plot();
+      } else {
+        Plotly.plot('violin_plot', violin_obj, root.modebar_options);
+      }
+    });
 
     // Histogram
     var hist_trace = {
@@ -1091,9 +1121,16 @@
           b: 60
       }
     };
-    Plotly.newPlot('histogram', data, layout, root.modebar_options)
 
-    update_histogram_width()
+    $('.histogram_tab').click(function() {
+      if ($('#histogram').hasClass('js-plotly-plot')){
+        redraw_histogram();
+        update_histogram_width();
+      } else {
+        Plotly.newPlot('histogram', data, layout, root.modebar_options)
+        update_histogram_width()
+      }
+    });
 
     $('.histogram_samples_group').val(root.stats_group);
     $('.histogram_samples_group').change(function() {
@@ -1119,13 +1156,18 @@
 
     root.prob_plot_group = 'samples_primary';
     $('.prob_plot_samples_group').val(root.prob_plot_group);
+    $('.prob_plot_tab').click(function() {
+      return redraw_prob_plot();
+    });
     $('.prob_plot_samples_group').change(function() {
       root.prob_plot_group = $(this).val();
       return redraw_prob_plot();
     });
 
-    make_table();
-    edit_data_change();
+    $('.stats_panel').click(function() {
+      make_table();
+      edit_data_change();
+    });
     $('#edit_sample_lists').change(edit_data_change);
     $('.edit_sample_value').change(edit_data_change);
     $('#block_by_index').click(edit_data_change);
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 daa5b3f2..4e82fff2 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -154,36 +154,12 @@
     };
   })(this));
 
-  $("#pylmm_mapping_compute").on("mouseover", (function(_this) {
-    return function() {
-      if ($(".outlier").length && $(".outlier-alert").length < 1) {
-        return showalert(outlier_text, "alert-success outlier-alert");
-      }
-    };
-  })(this));
-
-  $("#pylmm_compute").on("click", (function(_this) {
-    return function() {
-      var form_data, url;
-      //$("#progress_bar_container").modal();
-      url = "/loading";
-      $('input[name=method]').val("pylmm");
-      $('input[name=genofile]').val($('#genofile_pylmm').val());
-      $('input[name=num_perm]').val($('input[name=num_perm_pylmm]').val());
-      $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_pylmm]:checked').val());
-      form_data = $('#trait_data_form').serialize();
-      console.log("form_data is:", form_data);
-      return submit_special(url);
-      //return do_ajax_post(url, form_data);
-    };
-  })(this));
-
   $("#rqtl_geno_compute").on("click", (function(_this) {
     return function() {
       var form_data, url;
-      //$("#progress_bar_container").modal();
       url = "/loading";
       $('input[name=method]').val("rqtl_geno");
+      $('input[name=selected_chr]').val($('#chr_rqtl_geno').val());
       $('input[name=genofile]').val($('#genofile_rqtl_geno').val());
       $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val());
       $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val());
@@ -203,7 +179,6 @@
       }
       else {
         return submit_special(url);
-        //return do_ajax_post(url, form_data);
       }
     };
   })(this));
@@ -214,6 +189,7 @@
       console.log("RUNNING GEMMA");
       url = "/loading";
       $('input[name=method]').val("gemma");
+      $('input[name=selected_chr]').val($('#chr_gemma').val());
       $('input[name=num_perm]').val(0);
       $('input[name=genofile]').val($('#genofile_gemma').val());
       $('input[name=maf]').val($('input[name=maf_gemma]').val());
@@ -230,6 +206,7 @@
       //$("#progress_bar_container").modal();
       url = "/loading";
       $('input[name=method]').val("reaper");
+      $('input[name=selected_chr]').val($('#chr_reaper').val());
       $('input[name=genofile]').val($('#genofile_reaper').val());
       $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val());
       $('input[name=control_marker]').val($('input[name=control_reaper]').val());
diff --git a/wqflask/wqflask/static/new/javascript/stats.js b/wqflask/wqflask/static/new/javascript/stats.js
index 4f99982e..356d1cb0 100644
--- a/wqflask/wqflask/static/new/javascript/stats.js
+++ b/wqflask/wqflask/static/new/javascript/stats.js
@@ -154,16 +154,4 @@ Stats = (function() {
 
 })();
 
-bxd_only = new Stats([3, 5, 7, 8]);
-
-console.log("[xred] bxd_only mean:", bxd_only.mean());
-
-console.log("[xgreen] bxd_only median:", bxd_only.median());
-
-console.log("[xpurple] bxd_only std_dev:", bxd_only.std_dev());
-
-console.log("[xmagenta] bxd_only std_error:", bxd_only.std_error());
-
-console.log("[xyellow] bxd_only min:", bxd_only.min());
-
 window.Stats = Stats;
diff --git a/wqflask/wqflask/templates/mapping_results.html b/wqflask/wqflask/templates/mapping_results.html
index 5fb2c95e..00d725ea 100644
--- a/wqflask/wqflask/templates/mapping_results.html
+++ b/wqflask/wqflask/templates/mapping_results.html
@@ -257,7 +257,7 @@
         <div style="width: 100%;">
           <h2>Interval Analyst</h2>
           <div id="table_container">
-          <table id="interval_analyst" class="table table-hover table-striped nowrap">
+          <table id="interval_analyst" class="table-hover table-striped cell-border" style="float: left; width:100%;">
             <thead>
               <tr>
                 {% for header in gene_table_header %}
@@ -355,9 +355,7 @@
                 "autoWidth": false,
                 "deferRender": true,
                 "bSortClasses": false,
-                "scrollY": "600px",
                 "scrollCollapse": false,
-                "scroller": true,
                 "paging": false
             } );
 
@@ -372,7 +370,6 @@
                 "autoWidth": false,
                 "deferRender": true,
                 "bSortClasses": false,
-                "scrollY": "600px",
                 "scrollCollapse": false,
                 "paging": false
             } );
diff --git a/wqflask/wqflask/templates/search_result_page.html b/wqflask/wqflask/templates/search_result_page.html
index 9ad8a53e..a325ec9f 100644
--- a/wqflask/wqflask/templates/search_result_page.html
+++ b/wqflask/wqflask/templates/search_result_page.html
@@ -4,6 +4,7 @@
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/scroller.dataTables.min.css">
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
@@ -84,9 +85,9 @@
                         <th></th>
                     {% for header in header_fields %}
                         {% if header == 'Max LRS' %}
-                        <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+                        <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>
                         {% elif header == 'Additive Effect' %}
-                        <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+                        <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>
                         {% else %}
                         <th data-export="{{header}}">{{header}}</th>
                         {% endif %}
@@ -99,9 +100,9 @@
                         <th></th>
                     {% for header in header_fields %}
                         {% if header == 'Max LRS' %}
-                        <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+                        <th data-export="Max LRS">Max LRS <a href="http://genenetwork.org//glossary.html#LRS" target="_blank" style="color: white;"><sup>?</sup></a></th>
                         {% elif header == 'Additive Effect' %}
-                        <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank"><img style="width: 15px; height: 15px;" src="/static/new/images/question_mark.jpg"></a></th>
+                        <th data-export="Additive Effect">Additive Effect <a href="http://genenetwork.org//glossary.html#A" target="_blank" style="color: white;"><sup>?</sup></a></th>
                         {% else %}
                         <th data-export="{{header}}">{{header}}</th>
                         {% endif %}
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 8726226c..f5e81060 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -52,7 +52,7 @@
                     </div>
                 </div>    
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
+                    <div class="panel-heading stats_panel" data-toggle="collapse" data-parent="#accordion" data-target="#collapseTwo">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-down"></span> Statistics
                         </h3>
@@ -62,26 +62,38 @@
                             {% include 'show_trait_statistics.html' %}
                         </div>
                     </div>
-                </div>                
+                </div>
                 <div class="panel panel-default">
                     <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseThree">
                         <h3 class="panel-title">
-                             <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations
+                             <span class="glyphicon glyphicon-chevron-down"></span> Transform and Filter Data
                         </h3>
                     </div>
                     <div id="collapseThree" class="panel-collapse collapse in">
                         <div class="panel-body">
+                            {% include 'show_trait_transform_and_filter.html' %}
+                        </div>
+                    </div>
+                </div>
+                <div class="panel panel-default">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour">
+                        <h3 class="panel-title">
+                             <span class="glyphicon glyphicon-chevron-down"></span> Calculate Correlations
+                        </h3>
+                    </div>
+                    <div id="collapseFour" class="panel-collapse collapse in">
+                        <div class="panel-body">
                             {% include 'show_trait_calculate_correlations.html' %}
                         </div>
                     </div>
                 </div>                
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFour">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-down"></span> Mapping Tools
                         </h3>
                     </div>
-                    <div id="collapseFour" class="panel-collapse collapse in">
+                    <div id="collapseFive" class="panel-collapse collapse in">
                         <div class="panel-body">
                             {% include 'show_trait_mapping_tools.html' %}
                         </div>
@@ -89,12 +101,12 @@
                     </div>
                 </div>                
                 <div class="panel panel-default">
-                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseFive" aria-expanded="true">
+                    <div class="panel-heading" data-toggle="collapse" data-parent="#accordion" data-target="#collapseSix" aria-expanded="true">
                         <h3 class="panel-title">
                              <span class="glyphicon glyphicon-chevron-up"></span> Review and Edit Data
                         </h3>
                     </div>
-                    <div id="collapseFive" class="panel-collapse collapse" aria-expanded="true">
+                    <div id="collapseSix" class="panel-collapse collapse" aria-expanded="true">
                         <div class="panel-body">
                             {% include 'show_trait_edit_data.html' %}
                         </div>
@@ -210,7 +222,7 @@
                     "iDisplayLength": -1,
                     "autoWidth": true,
                     "bLengthChange": true,
-                    "bDeferRender": true,
+                    "deferRender": false,
                     "bSortClasses": false,
                     "scrollY": "600px",
                     "scrollCollapse": false,
@@ -221,7 +233,7 @@
                 } );
 
                 {% else %}
-                    
+
                 $('#samples_primary, #samples_other').DataTable( {
                     "columns": [
                         { "bSortable": false, "width": "8%" },
@@ -242,7 +254,7 @@
                     "iDisplayLength": -1,
                     "autoWidth": true,
                     "bLengthChange": true,
-                    "bDeferRender": true,
+                    "deferRender": false,
                     "bSortClasses": false,
                     "scrollY": "600px",
                     "scrollCollapse": false,
@@ -251,6 +263,7 @@
                     },
                     "paging": false
                 } );
+
                 {% endif %}
 
                 var slider = document.getElementById('p_range_slider');
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c1f8f824..0192bff1 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -5,10 +5,6 @@
     </tr>
     {% if this_trait.dataset.type == 'Publish' %}
     <tr>
-        <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>
@@ -24,6 +20,11 @@
         <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>
+    {% else %}
+    <tr>
+        <td>Tissue</td>
+        <td>{{ this_trait.dataset.tissue }}</td>
+    </tr>
     {% endif %}
     {% if this_trait.dataset.type == 'ProbeSet' %}
     {% if this_trait.symbol != None %}
diff --git a/wqflask/wqflask/templates/show_trait_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index cfcf2ce5..ab134663 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -1,6 +1,7 @@
 <div>
     <!--<h2>Review and Edit Data</h2>-->
 
+<!--
     <div class="well form-horizontal">
         <fieldset id="showHideOptions">
             <legend>Block samples</legend>
@@ -59,11 +60,6 @@
                 <option value="sqrt">Square Root</option>
               </select>
               </div>
-              <!--
-              {% if sample_groups[0].sample_qnorm is not none %}
-              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
-              {% endif %}
-              -->
             </div>
         </fieldset>
         <br>
@@ -81,7 +77,7 @@
         </div>
     </div>
     <br>
-
+-->
 
     <!--<div id="edit_sample_lists">-->
     {% for sample_type in sample_groups %}
@@ -94,7 +90,7 @@
                 <thead>
                     <tr>
                         <th></th>
-                        <th>Index</th>
+                        <th>ID</th>
                         <th>Sample</th>
                         <th style="text-align: right;">Value</th>
                         {% if sample_type.se_exists() %}
@@ -113,7 +109,7 @@
                 </thead>
                 <tbody>
                     {% for sample in sample_type.sample_list %}
-                    <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}">
+                    <tr class="{{ sample.class_outlier }} value_se" id="{% if outer_loop.index == 1 %}Primary_{{ sample.this_id }}{% else %}Other_{{ sample.this_id }}{% endif %}">
                         <td align="center" style="padding-left: 0px; padding-right: 0px;" class="column_name-"><input type="checkbox" name="selectCheck" class="checkbox edit_sample_checkbox" value="{{ sample.name }}" checked="checked">
                         </td>
                         <td class="column_name-Index" align="right">{{ loop.index }}</td>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 8e003897..e0bc8eb8 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -14,11 +14,6 @@
                 <li>
                     <a href="#rqtl_geno" data-toggle="tab">R/qtl</a>
                 </li>
-<!--
-                <li>
-                    <a href="#pylmm" data-toggle="tab">pyLMM</a>
-                </li>
--->
                 {% endif %}
                 {% for mapping_method in dataset.group.mapping_names %}
                 {% if mapping_method == "GEMMA" %}
@@ -39,6 +34,16 @@
             <div class="tab-content">
                 <div class="tab-pane active" id="gemma">
                     <div style="padding-top: 20px;" class="form-horizontal">
+                        <div class="mapping_method_fields form-group">
+                            <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
+                            <div style="margin-left:20px;" class="col-xs-2 controls">
+                                <select id="chr_gemma" class="form-control">
+                                    {% for item in chr_list %}
+                                    <option value="{{ item[1] }}">{{ item[0] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
                             <label for="genofiles" style="text-align: right;" class="col-xs-3 control-label">Genotypes</label>
@@ -61,11 +66,11 @@
                             <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>
@@ -110,6 +115,16 @@
                 {% if dataset.group.mapping_id == "1" %}
                 <div class="tab-pane" id="interval_mapping">
                     <div style="margin-top: 20px" class="form-horizontal">
+                        <div class="mapping_method_fields form-group">
+                            <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
+                            <div style="margin-left:20px;" class="col-xs-2 controls">
+                                <select id="chr_reaper" class="form-control">
+                                    {% for item in chr_list %}
+                                    <option value="{{ item[1] }}">{{ item[0] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
                             <label style="text-align: right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
@@ -202,6 +217,16 @@
                 </div>
                 <div class="tab-pane" id="rqtl_geno">
                     <div style="margin-top: 20px" class="form-horizontal">
+                        <div class="mapping_method_fields form-group">
+                            <label for="chr_select" style="text-align: right;" class="col-xs-3 control-label">Chromosome</label>
+                            <div style="margin-left:20px;" class="col-xs-2 controls">
+                                <select id="chr_rqtl_geno" class="form-control">
+                                    {% for item in chr_list %}
+                                    <option value="{{ item[1] }}">{{ item[0] }}</option>
+                                    {% endfor %}
+                                </select>
+                            </div>
+                        </div>
                         {% if genofiles and genofiles|length>0 %}
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:right;" for="genofiles" class="col-xs-3 control-label">Genotypes</label>
@@ -304,30 +329,6 @@
                         </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 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 %}
-                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
-                                    {% endfor %}
-                                </select>
-                            </div>
-                        </div>
-                        {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <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>
-                            </div>
-                        </div>
-                    </div>
-                </div>
                 {% endif %}
             </div>
         </div>
@@ -341,10 +342,6 @@
              <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>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>
--->
              {% endif %}
         </dl>
     </div>
diff --git a/wqflask/wqflask/templates/show_trait_statistics.html b/wqflask/wqflask/templates/show_trait_statistics.html
index ac0c753a..a0bdc987 100644
--- a/wqflask/wqflask/templates/show_trait_statistics.html
+++ b/wqflask/wqflask/templates/show_trait_statistics.html
@@ -5,15 +5,15 @@
                     <a href="#stats_tab" data-toggle="tab">Basic Statistics</a>
                 </li>
                 <li>
-                    <a href="#histogram_tab" data-toggle="tab">Histogram</a>
+                    <a href="#histogram_tab" class="histogram_tab" data-toggle="tab">Histogram</a>
                 </li>
                 {% if num_values < 256 %}
                 <li>
-                    <a href="#bar_chart_tab" data-toggle="tab">Bar Chart</a>
+                    <a href="#bar_chart_tab" class="bar_chart_tab" data-toggle="tab">Bar Chart</a>
                 </li>
                 {% endif %}
                 <li>
-                    <a href="#probability_plot" data-toggle="tab">Probability Plot</a>
+                    <a href="#probability_plot" class="prob_plot_tab" data-toggle="tab">Probability Plot</a>
                 </li>
                 {% if g.user_session.logged_in %}
                 <li>
@@ -21,10 +21,10 @@
                 </li>
                 {% endif %}
                 <li>
-                    <a href="#box_plot_tab" data-toggle="tab">Box Plot</a>
+                    <a href="#box_plot_tab" class="box_plot_tab" data-toggle="tab">Box Plot</a>
                 </li>
                 <li>
-                    <a href="#violin_plot_tab" data-toggle="tab">Violin Plot</a>
+                    <a href="#violin_plot_tab" class="violin_plot_tab" data-toggle="tab">Violin Plot</a>
                 </li>
             </ul>
 
diff --git a/wqflask/wqflask/templates/show_trait_transform_and_filter.html b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
new file mode 100644
index 00000000..5d14a30e
--- /dev/null
+++ b/wqflask/wqflask/templates/show_trait_transform_and_filter.html
@@ -0,0 +1,79 @@
+<div>
+    <div class="form-horizontal">
+            <legend>Block samples</legend>
+            <p>Edit or delete values in the Trait Data boxes, and use the
+                <strong>Reset</strong> option as
+                needed.
+            </p>
+
+            <div id="blockMenuSpan" class="input-append" style="margin-bottom: 10px;">
+                <label for="remove_samples_field">Block samples by index:</label>
+                <input type="text" id="remove_samples_field">
+                <select id="block_group" size="1">
+                  <option value="primary">
+                    {{ sample_group_types['samples_primary'] }}
+                  </option>
+                  <option value="other">
+                    {{ sample_group_types['samples_other'] }}
+                  </option>
+                </select>
+                <input type="button" id="block_by_index" class="btn" value="Block">
+            </div>
+            <div id="remove_samples_invalid" class="alert alert-error" style="display:none;">
+                  Please check that your input is formatted correctly, e.g. <strong>3, 5-10, 12</strong>
+            </div>
+            {% if sample_groups[0].attributes %}
+            <div class="input-append" style="margin-top:10px; margin-bottom:10px;">
+                <label for="exclude_menu">Block samples by group:</label>
+                <select id="exclude_menu" size=1>
+                  {% for attribute in sample_groups[0].attributes %}
+                  <option value="{{ sample_groups[0].attributes[attribute].name.replace(' ', '_') }}">
+                      {{ sample_groups[0].attributes[attribute].name }}</option>
+                  {% endfor %}
+                </select>
+                <select id="attribute_values" size=1>
+                </select>
+                <input type="button" id="exclude_group" class="btn" value="Block">
+            </div>
+            {% endif %}
+            <div>
+              <input type="button" id="hide_no_value" class="btn btn-default" value="Hide No Value">
+              <input type="button" id="block_outliers" class="btn btn-default" value="Block Outliers">
+              <input type="button" id="reset" class="btn btn-primary" value="Reset">
+              <span class="input-append">
+                <input type="button" id="export" class="btn btn-default" value="Export">
+                <select id="export_format" class="select optional span2">
+                  <option value="excel">Excel</option>
+                  <option value="csv">CSV</option>
+                </select>
+              </span>
+              <br>
+              <div style="margin-top:10px;">
+              <input type="button" id="normalize" class="btn btn-default" value="Normalize">
+              <select id="norm_method" class="select optional span2">
+                <option value="log2">Log2</option>
+                <option value="qnorm">Quantile</option>
+                <option value="sqrt">Square Root</option>
+              </select>
+              </div>
+              <!--
+              {% if sample_groups[0].sample_qnorm is not none %}
+              <input type="button" id="qnorm" class="btn btn-default" value="Quantile Normalize">
+              {% endif %}
+              -->
+            </div>
+        <br>
+
+        <div>
+            <p>Outliers highlighted in
+                    <strong style="background-color:yellow;">yellow</strong>
+                    can be hidden using
+                    the <strong>Hide Outliers</strong> button.
+            </p>
+
+            <p>Samples with no value (x) can be hidden by clicking
+                    <strong>Hide No Value</strong> button.
+            </p>
+        </div>
+    </div>
+</div>
\ No newline at end of file