- Changed the way the genofile is set so different genofiles can be selected for mapping

- Now shows error page for Correlation Matrix if traits aren't all from the same group (later need to make it check for shared samples, since different groups may contain some of the same samples
- Mapping results page now displays the genofile in the information section
- Only show Interval Analyst if species is mouse or rat (previously it would show a blank table for other species)
- Network Graph now only shows links in a node's info if the relevant information (for example geneid) exists, and the label changes depending on the type of data set
- Other minor changes to the appearance of the Network Graph menu (less white space, plus clickable descriptions for a couple options)
- Improved Correlations Results page to shorten Description and Authors cell content for Phenotype traits (to keep table width manageable)
- Changed the glossary links for LRS and Additive Effect columns for Gene Global Search
- Improved appearance for Phenotype Global Search results
- Temporarily removed Mapping options/features that don't work from the trait page

15 files changed, 213 insertions, 203 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 4959457a..dbdbb51c 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -169,7 +169,7 @@ def mescape(*items):
 class Markers(object):
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
     def __init__(self, name):
-        json_data_fh = open(locate(name + '.json','genotype/json'))
+        json_data_fh = open(locate(name + ".json",'genotype/json'))
         try:
             markers = json.load(json_data_fh)
         except:
@@ -334,7 +334,10 @@ class DatasetGroup(object):
         else:
             marker_class = Markers            
 
-        self.markers = marker_class(self.name)
+        if self.genofile:
+            self.markers = marker_class(self.genofile[:-5])
+        else:
+            self.markers = marker_class(self.name)
 
     def get_f1_parent_strains(self):
         try:
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 95a5f6a6..b34beb7b 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -72,7 +72,14 @@ class CorrelationMatrix(object):
 
         self.all_sample_list = []
         self.traits = []
+        self.insufficient_shared_samples = False
+        this_group = self.trait_list[0][1].group.name #ZS: Getting initial group name before verifying all traits are in the same group in the following loop
         for trait_db in self.trait_list:
+            if trait_db[1].group.name != this_group:
+                self.insufficient_shared_samples = True
+                break
+            else:
+                this_group = trait_db[1].group.name
             this_trait = trait_db[0]
             self.traits.append(this_trait)
             this_sample_data = this_trait.data
@@ -81,100 +88,102 @@ class CorrelationMatrix(object):
                 if sample not in self.all_sample_list:
                     self.all_sample_list.append(sample)
 
-        self.sample_data = []
-        for trait_db in self.trait_list:
-            this_trait = trait_db[0]
-            this_sample_data = this_trait.data
-
-            this_trait_vals = []
-            for sample in self.all_sample_list:
-                if sample in this_sample_data:
-                    this_trait_vals.append(this_sample_data[sample].value)
-                else:
-                    this_trait_vals.append('')
-            self.sample_data.append(this_trait_vals)
+        if self.insufficient_shared_samples:
+            pass
+        else:
+            self.sample_data = []
+            for trait_db in self.trait_list:
+                this_trait = trait_db[0]
+                this_sample_data = this_trait.data
 
-        if len(this_trait_vals) < len(self.trait_list): #Shouldn't do PCA if there are more traits than observations/samples
-            return False
+                this_trait_vals = []
+                for sample in self.all_sample_list:
+                    if sample in this_sample_data:
+                        this_trait_vals.append(this_sample_data[sample].value)
+                    else:
+                        this_trait_vals.append('')
+                self.sample_data.append(this_trait_vals)
 
-        self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
+            if len(this_trait_vals) < len(self.trait_list): #Shouldn't do PCA if there are more traits than observations/samples
+                return False
 
-        self.corr_results = []
-        self.pca_corr_results = []
-        self.trait_data_array = []
-        for trait_db in self.trait_list:
-            this_trait = trait_db[0]
-            this_db = trait_db[1]
+            self.lowest_overlap = 8 #ZS: Variable set to the lowest overlapping samples in order to notify user, or 8, whichever is lower (since 8 is when we want to display warning)
 
-            this_db_samples = this_db.group.all_samples_ordered()
-            this_sample_data = this_trait.data
+            self.corr_results = []
+            self.pca_corr_results = []
+            self.trait_data_array = []
+            for trait_db in self.trait_list:
+                this_trait = trait_db[0]
+                this_db = trait_db[1]
 
-            this_trait_vals = []
-            for index, sample in enumerate(this_db_samples):
-                if (sample in this_sample_data):
-                    sample_value = this_sample_data[sample].value
-                    this_trait_vals.append(sample_value)
-            self.trait_data_array.append(this_trait_vals)
-
-            corr_result_row = []
-            pca_corr_result_row = []
-            is_spearman = False #ZS: To determine if it's above or below the diagonal
-            for target in self.trait_list:
-                target_trait = target[0]
-                target_db = target[1]
-                target_samples = target_db.group.all_samples_ordered()
-                target_sample_data = target_trait.data
+                this_db_samples = this_db.group.all_samples_ordered()
+                this_sample_data = this_trait.data
 
                 this_trait_vals = []
-                target_vals = []
-                for index, sample in enumerate(target_samples):
-                    if (sample in this_sample_data) and (sample in target_sample_data):
+                for index, sample in enumerate(this_db_samples):
+                    if (sample in this_sample_data):
                         sample_value = this_sample_data[sample].value
-                        target_sample_value = target_sample_data[sample].value
                         this_trait_vals.append(sample_value)
-                        target_vals.append(target_sample_value)
-
-                this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals)
-
-                if num_overlap < self.lowest_overlap:
-                    self.lowest_overlap = num_overlap
-                if num_overlap == 0:
-                    corr_result_row.append([target_trait, 0, num_overlap])
-                    pca_corr_result_row.append(0)
-                else:
-                    pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
-                    if is_spearman == False:
-                        sample_r, sample_p = pearson_r, pearson_p
-                        if sample_r == 1:
-                            is_spearman = True
+                self.trait_data_array.append(this_trait_vals)
+
+                corr_result_row = []
+                pca_corr_result_row = []
+                is_spearman = False #ZS: To determine if it's above or below the diagonal
+                for target in self.trait_list:
+                    target_trait = target[0]
+                    target_db = target[1]
+                    target_samples = target_db.group.all_samples_ordered()
+                    target_sample_data = target_trait.data
+
+                    this_trait_vals = []
+                    target_vals = []
+                    for index, sample in enumerate(target_samples):
+                        if (sample in this_sample_data) and (sample in target_sample_data):
+                            sample_value = this_sample_data[sample].value
+                            target_sample_value = target_sample_data[sample].value
+                            this_trait_vals.append(sample_value)
+                            target_vals.append(target_sample_value)
+
+                    this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(this_trait_vals, target_vals)
+
+                    if num_overlap < self.lowest_overlap:
+                        self.lowest_overlap = num_overlap
+                    if num_overlap == 0:
+                        corr_result_row.append([target_trait, 0, num_overlap])
+                        pca_corr_result_row.append(0)
                     else:
-                        sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
-
-                    corr_result_row.append([target_trait, sample_r, num_overlap])
-                    pca_corr_result_row.append(pearson_r)
+                        pearson_r, pearson_p = scipy.stats.pearsonr(this_trait_vals, target_vals)
+                        if is_spearman == False:
+                            sample_r, sample_p = pearson_r, pearson_p
+                            if sample_r == 1:
+                                is_spearman = True
+                        else:
+                            sample_r, sample_p = scipy.stats.spearmanr(this_trait_vals, target_vals)
 
-            self.corr_results.append(corr_result_row)
-            self.pca_corr_results.append(pca_corr_result_row)
+                        corr_result_row.append([target_trait, sample_r, num_overlap])
+                        pca_corr_result_row.append(pearson_r)
 
-        corr_result_eigen = la.eigenvectors(numarray.array(self.pca_corr_results))
-        corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen)
+                self.corr_results.append(corr_result_row)
+                self.pca_corr_results.append(pca_corr_result_row)
 
-        groups = []
-        for sample in self.all_sample_list:
-            groups.append(1)
+            corr_result_eigen = la.eigenvectors(numarray.array(self.pca_corr_results))
+            corr_eigen_value, corr_eigen_vectors = sortEigenVectors(corr_result_eigen)
 
-        pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
+            groups = []
+            for sample in self.all_sample_list:
+                groups.append(1)
 
-        self.loadings_array = self.process_loadings()
+            pca = self.calculate_pca(range(len(self.traits)), corr_eigen_value, corr_eigen_vectors)
 
-        self.js_data = dict(traits = [trait.name for trait in self.traits],
-                            groups = groups,
-                            cols = range(len(self.traits)),
-                            rows = range(len(self.traits)),
-                            samples = self.all_sample_list,
-                            sample_data = self.sample_data,)
-        #                    corr_results = [result[1] for result in result_row for result_row in self.corr_results])
+            self.loadings_array = self.process_loadings()
 
+            self.js_data = dict(traits = [trait.name for trait in self.traits],
+                                groups = groups,
+                                cols = range(len(self.traits)),
+                                rows = range(len(self.traits)),
+                                samples = self.all_sample_list,
+                                sample_data = self.sample_data,)
+            #                    corr_results = [result[1] for result in result_row for result_row in self.corr_results])
         
     def get_trait_db_obs(self, trait_db_list):
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 8882c515..60424468 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -148,6 +148,10 @@ class MarkerRegression(object):
             self.showGenes = "ON"
             self.viewLegend = "ON"
 
+        if 'genofile' in start_vars:
+          if start_vars['genofile'] != "":
+            self.genofile_string = start_vars['genofile']
+            self.dataset.group.genofile = self.genofile_string.split(":")[0]
         self.dataset.group.get_markers()
         if self.mapping_method == "gemma":
             self.score_type = "-log(p)"
@@ -162,11 +166,10 @@ class MarkerRegression(object):
             self.mapping_scale = "morgan"
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
-            self.dataset.group.genofile = start_vars['genofile']
             self.method = start_vars['mapmethod_rqtl_geno']
             self.model = start_vars['mapmodel_rqtl_geno']
-            if start_vars['pair_scan'] == "true":
-                self.pair_scan = True
+            #if start_vars['pair_scan'] == "true":
+            #    self.pair_scan = True
             if self.permCheck and self.num_perm > 0:
                 self.perm_output, self.suggestive, self.significant, results = rqtl_mapping.run_rqtl_geno(self.vals, self.dataset, self.method, self.model, self.permCheck, self.num_perm, self.do_control, self.control_marker, self.manhattan_plot, self.pair_scan)
             else:
@@ -198,7 +201,6 @@ class MarkerRegression(object):
 
             self.control_marker = start_vars['control_marker']
             self.do_control = start_vars['do_control']
-            self.dataset.group.genofile = start_vars['genofile']
             logger.info("Running qtlreaper")
             results, self.json_data, self.perm_output, self.suggestive, self.significant, self.bootstrap_results = qtlreaper_mapping.gen_reaper_results(self.this_trait,
                                                                                                                                                         self.dataset,
@@ -217,7 +219,6 @@ class MarkerRegression(object):
             #results = self.run_plink()
         elif self.mapping_method == "pylmm":
             logger.debug("RUNNING PYLMM")
-            self.dataset.group.genofile = start_vars['genofile']
             if self.num_perm > 0:
                 self.run_permutations(str(temp_uuid))
             results = self.gen_data(str(temp_uuid))
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 82a44796..d99ac074 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -171,6 +171,8 @@ class MarkerRegression(object):
         self.dataset = start_vars['dataset']
         self.this_trait = start_vars['this_trait']
         self.species = start_vars['species']
+        if 'genofile_string' in start_vars:
+            self.genofile_string = start_vars['genofile_string']
 
         #Needing for form submission when doing single chr mapping or remapping after changing options
         self.samples = start_vars['samples']
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index cebe5c03..4ce6c48d 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -181,12 +181,21 @@ class NetworkGraph(object):
                                  
                     self.edges_list.append(edge_dict)
       
-            node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name), 
-                                    'label' : this_trait.name,
-                                    'symbol' : this_trait.symbol,
-                                    'geneid' : this_trait.geneid,
-                                    'omim' : this_trait.omim,
-                                    'max_corr' : max_corr } }
+            if trait_db[1].type == "ProbeSet":
+                node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                        'label' : this_trait.symbol,
+                                        'symbol' : this_trait.symbol,
+                                        'geneid' : this_trait.geneid,
+                                        'omim' : this_trait.omim,
+                                        'max_corr' : max_corr } }
+            elif trait_db[1].type == "Publish":
+                node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                        'label' : this_trait.name,
+                                        'max_corr' : max_corr } }
+            else:
+                node_dict = { 'data' : {'id' : str(this_trait.name) + ":" + str(this_trait.dataset.name),
+                                        'label' : this_trait.name,
+                                        'max_corr' : max_corr } }
             self.nodes_list.append(node_dict)
       
         #self.network_data['dataSchema'] = {'nodes' : [{'name' : "label" , 'type' : "string"}],
@@ -211,7 +220,6 @@ class NetworkGraph(object):
         #                    corr_results = [result[1] for result in result_row for result_row in self.corr_results])
 
     def get_trait_db_obs(self, trait_db_list):
-
         self.trait_list = []
         for i, trait_db in enumerate(trait_db_list):
             if i == (len(trait_db_list) - 1):
diff --git a/wqflask/wqflask/static/new/css/network_graph.css b/wqflask/wqflask/static/new/css/network_graph.css
index 1cba546a..1a0bafeb 100644
--- a/wqflask/wqflask/static/new/css/network_graph.css
+++ b/wqflask/wqflask/static/new/css/network_graph.css
@@ -14,7 +14,6 @@
     position: relative;
     float: left;
     width: 18.5em;
-    padding: 1em 1em 1em 1em;
     background: #fff url('/static/new/images/a1.gif') top right repeat-y;
 }
 
diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js
index d1afd47c..731acf1a 100644
--- a/wqflask/wqflask/static/new/javascript/network_graph.js
+++ b/wqflask/wqflask/static/new/javascript/network_graph.js
@@ -12,7 +12,7 @@ window.onload=function() {
             selector: 'node',
             style: {
               'background-color': '#666',
-              'label': 'data(symbol)',
+              'label': 'data(label )',
               'font-size': 10
             }
           },
@@ -81,10 +81,18 @@ window.onload=function() {
     function create_qtips(cy){
         cy.nodes().qtip({
                             content: function(){
+                                qtip_content = ''
                                 gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
-                                ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>' 
-                                omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>' 
-                                qtip_content = gn_link + ncbi_link + omim_link
+                                qtip_content += gn_link
+                                if (typeof(this.data().geneid) !== 'undefined'){
+                                    ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>'
+                                    qtip_content += ncbi_link
+                                }
+                                if (typeof(this.data().omim) !== 'undefined'){
+                                    omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>'
+                                    qtip_content += omim_link
+                                }
+                                //qtip_content = gn_link + ncbi_link + omim_link
                                 return qtip_content
                                 //return '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'<a>'+'</b>' 
                             },
diff --git a/wqflask/wqflask/templates/correlation_matrix.html b/wqflask/wqflask/templates/correlation_matrix.html
index eb675568..ab793d58 100644
--- a/wqflask/wqflask/templates/correlation_matrix.html
+++ b/wqflask/wqflask/templates/correlation_matrix.html
@@ -64,21 +64,15 @@
 <br>
 <br>
 <h2>Factor Loadings Plot</h2>
-<div id="loadings_plot"></div>
-
+<div id="loadings_plot" style="margin-top: 20px; margin-bottom: 20px; width: 980px; border-style: solid; border-width: 1px;"></div>
 <h2>Factor Loadings Table</h2>
-<table class="table table-hover table-striped" border="1" id='trait_table' style="margin: 20px;" width="40%">
+<table class="table table-hover table-striped" border="1" style="margin-top: 20px; margin-bottom: 20px;" width="30%">
   <thead>
     <tr>
       <th></th>
-      <th align="right" >Factor 1</th>
-      <th align="right" >Factor 2</th>
-      {% if trait_list|length > 2 %}<th align="right" >Factor 3</th>{% endif %}
-<!--
-      {% for row in loadings_array %}
-      <th>Factor {{ loop.index }}</th>
-      {% endfor %}
--->
+      <th style="text-align: right;" >Factor 1</th>
+      <th style="text-align: right;" >Factor 2</th>
+      {% if trait_list|length > 2 %}<th style="text-align: right;">Factor 3</th>{% endif %}
     </tr>
   </thead>
   <tbody>
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index fbf373f6..fa9e3585 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -383,8 +383,8 @@
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
-                    { "type": "natural", "width": "25%" },
-                    { "type": "natural", "width": "15%" },
+                    { "type": "natural", "width": "20%" },
+                    { "type": "natural", "width": "12%" },
                     { "type": "natural" },
                     { "type": "natural" },
                     { "type": "natural" },
@@ -394,9 +394,14 @@
                     { "type": "scientific" }
                 ],
                 "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(3).attr('title', $('td', row).eq(3).text());
+                    if ($('td', row).eq(3).text().length > 50) {
+                        $('td', row).eq(3).text($('td', row).eq(3).text().substring(0, 50));
+                        $('td', row).eq(3).text($('td', row).eq(3).text() + '...')
+                    }
                     $('td', row).eq(4).attr('title', $('td', row).eq(4).text());
-                    if ($('td', row).eq(4).text().length > 60) {
-                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 60));
+                    if ($('td', row).eq(4).text().length > 40) {
+                        $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 40));
                         $('td', row).eq(4).text($('td', row).eq(4).text() + '...')
                     }
                 },
diff --git a/wqflask/wqflask/templates/empty_collection.html b/wqflask/wqflask/templates/empty_collection.html
deleted file mode 100644
index 3f2b3786..00000000
--- a/wqflask/wqflask/templates/empty_collection.html
+++ /dev/null
@@ -1,15 +0,0 @@
-{% extends "base.html" %}
-{% block title %}{{ tool }}{% endblock %}
-{% block content %}
-<!-- Start of body -->
-    {{ header("Error") }}
-
-    <div class="container">
-        <input type="hidden" name="uc_id" id="uc_id" value="{{ uc_id }}">
-        <p>You must select at least one trait to use the {{ tool }}.</p>
-    </div>
-
-
-<!-- End of body -->
-
-{% endblock %}
diff --git a/wqflask/wqflask/templates/gsearch_gene.html b/wqflask/wqflask/templates/gsearch_gene.html
index e8bb6337..c1f039c7 100644
--- a/wqflask/wqflask/templates/gsearch_gene.html
+++ b/wqflask/wqflask/templates/gsearch_gene.html
@@ -42,9 +42,9 @@
                     <th data-export="Description">Description</th> 
                     <th data-export="Location">Location</th>
                     <th data-export="Mean">Mean</th>
-                    <th data-export="Max LRS">Max LRS<a href="http://genenetwork.org/glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                    <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 Location">Max LRS Location</th>
-                    <th data-export="Additive Effect">Additive <a href="http://genenetwork.org/glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                    <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>
                   </tr>
                 </thead> 
                 <tbody>
@@ -80,9 +80,9 @@
                     <th>Description</th> 
                     <th>Location</th>
                     <th>Mean</th>
-                    <th>Max LRS<a href="http://genenetwork.org/glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
-                    <th>Max LRS Location</th>
-                    <th>Additive <a href="http://genenetwork.org/glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                    <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="LRS Location">Max LRS Location</th>
+                    <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>
                   </tr>
                 </tfoot> 
               </table>
@@ -102,8 +102,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
 	
     <script type="text/javascript" charset="utf-8">
         $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
diff --git a/wqflask/wqflask/templates/gsearch_pheno.html b/wqflask/wqflask/templates/gsearch_pheno.html
index 2f7dcaf6..1bb2120e 100644
--- a/wqflask/wqflask/templates/gsearch_pheno.html
+++ b/wqflask/wqflask/templates/gsearch_pheno.html
@@ -2,16 +2,13 @@
 {% block title %}Search Results{% endblock %}
 {% block css %}
     <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/css/jquery.dataTables.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/DT_bootstrap/DT_bootstrap.css" />
-    <link rel="stylesheet" type="text/css" href="/static/packages/TableTools/media/css/TableTools.css" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/dataTables.fixedHeader.css" >
-    <link rel="stylesheet" type="text/css" href="//cdn.datatables.net/fixedcolumns/3.0.4/css/dataTables.fixedColumns.css">
 {% endblock %}
 {% block content %}
 <!-- Start of body -->
 
     <div class="container">
 
+        <p>You searched for {{ terms }}.</p>
         <p>To study a record, click on its ID below.<br />Check records below and click Add button to add to selection.</p>
 
         <div>
@@ -30,28 +27,28 @@
               <button class="btn btn-default" id="export_traits">Download CSV</button>
             </form>
             <br />
-            <div style="width: 1500px; background-color: #eeeeee; border: 1px solid black;">
-            <table width="1500px" id="trait_table" class="table table-hover table-striped">
+            v<div>
+              <table id="trait_table" class="table table-hover table-striped nowrap" style="float: left;">
                 <thead>
                     <tr>
-                        <th style="background-color: #eeeeee;"></th>
-                        <th data-export="Index" style="background-color: #eeeeee;">Index</th>
-                        <th data-export="Species" style="background-color: #eeeeee;">Species</th>
-                        <th data-export="Group" style="background-color: #eeeeee;">Group</th>
-                        <th data-export="Record" style="background-color: #eeeeee;">Record</th>
-                        <th data-export="Description" style="background-color: #eeeeee;">Description</th>
-                        <th data-export="Authors" style="background-color: #eeeeee;">Authors</th>
-                        <th data-export="Year" style="background-color: #eeeeee;">Year</th>
-                        <th data-export="LRS" style="background-color: #eeeeee; text-align: right;">Max&nbsp;&nbsp;<br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
-                        <th data-export="LRS Location" style="background-color: #eeeeee;">Max LRS Location</th>
-                        <th data-export="Additive Effect" style="background-color: #eeeeee; text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th></th>
+                        <th data-export="Index">Index</th>
+                        <th data-export="Species">Species</th>
+                        <th data-export="Group">Group</th>
+                        <th data-export="Record">Record</th>
+                        <th data-export="Description">Description</th>
+                        <th data-export="Authors">Authors</th>
+                        <th data-export="Year">Year</th>
+                        <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="LRS Location">Max LRS Location</th>
+                        <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>
                     </tr>
                 </thead>
                 <tbody>
                  {% for this_trait in trait_list %}
-                    <TR id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
-                        <td><INPUT TYPE="checkbox" NAME="searchResult" class="checkbox trait_checkbox" style="transform: scale(1.5);" VALUE="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
-                        <td data-export="{{ loop.index }}">{{ loop.index }}</td>
+                    <tr id="trait:{{ this_trait.name }}:{{ this_trait.dataset.name }}">
+                        <td align="center" style="padding-right: 0px; padding-left: 5px;"><input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="{{ data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name)) }}"></td>
+                        <td align="right" data-export="{{ loop.index }}">{{ loop.index }}</td>
                         <td data-export="{{ this_trait.dataset.group.species }}">{{ this_trait.dataset.group.species }}</td>
                         <td data-export="{{ this_trait.dataset.group.name }}">{{ this_trait.dataset.group.name }}</td>
                         <td data-export="{{ this_trait.name }}"><a href="{{ url_for('show_trait_page', trait_id = this_trait.name, dataset = this_trait.dataset.name)}}">{{ this_trait.name }}</a></td>
@@ -61,22 +58,22 @@
                         <td data-export="{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}" align="right">{% if this_trait.LRS_score_repr != "N/A" %}{{ '%0.1f' % this_trait.LRS_score_repr|float }}{% else %}N/A{% endif %}</td>
                         <td data-export="{{ this_trait.LRS_location_repr }}" align="right">{{ this_trait.LRS_location_repr }}</td>
                         <td data-export="{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}" align="right">{% if this_trait.additive != "" %}{{ this_trait.additive }}{% else %}N/A{% endif %}</td>
-                    </TR>
+                    </tr>
                 {% endfor %}
                 </tbody>
                 <tfoot>
                     <tr>
-                        <th style="background-color: #eeeeee;"></th>
-                        <th style="background-color: #eeeeee;">Index</th>
-                        <th style="background-color: #eeeeee;">Species</th>
-                        <th style="background-color: #eeeeee;">Group</th>
-                        <th style="background-color: #eeeeee;">Record</th>
-                        <th style="background-color: #eeeeee;">Description</th>
-                        <th style="background-color: #eeeeee;">Authors</th>
-                        <th style="background-color: #eeeeee;">Year</th>
-                        <th style="background-color: #eeeeee; text-align: right;">Max&nbsp;&nbsp;<br>LRS<a href="http://genenetwork.org//glossary.html#L" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
-                        <th style="background-color: #eeeeee;">Max LRS Location</th>
-                        <th style="background-color: #eeeeee; text-align: right;">Additive<br>Effect<a href="http://genenetwork.org//glossary.html#A" target="_blank"><sup style="color:#f00"> ?</sup></a></th>
+                        <th></th>
+                        <th>Index</th>
+                        <th>Species</th>
+                        <th>Group</th>
+                        <th>Record</th>
+                        <th>Description</th>
+                        <th>Authors</th>
+                        <th>Year</th>
+                        <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="LRS Location">Max LRS Location</th>
+                        <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>
                     </tr>
                 </tfoot>
             </table>
@@ -96,8 +93,6 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colReorder.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/extensions/dataTables.colResize.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
 	
     <script type="text/javascript" charset="utf-8">
         $.fn.dataTable.ext.order['dom-checkbox'] = function  ( settings, col )
@@ -117,6 +112,18 @@
 
             console.time("Creating table");
             $('#trait_table').DataTable( {
+                "createdRow": function ( row, data, index ) {
+                    $('td', row).eq(5).attr('title', $('td', row).eq(5).text());
+                    if ($('td', row).eq(5).text().length > 50) {
+                        $('td', row).eq(5).text($('td', row).eq(5).text().substring(0, 50));
+                        $('td', row).eq(5).text($('td', row).eq(5).text() + '...')
+                    }
+                    $('td', row).eq(6).attr('title', $('td', row).eq(6).text());
+                    if ($('td', row).eq(6).text().length > 50) {
+                        $('td', row).eq(6).text($('td', row).eq(6).text().substring(0, 50));
+                        $('td', row).eq(6).text($('td', row).eq(6).text() + '...')
+                    }
+                },
                 "paging": false,
                 "columns": [
                     { "orderDataType": "dom-checkbox" },
@@ -134,6 +141,7 @@
                 "columnDefs": [
                     {
                         "targets": 0,
+                        "orderable": false,
                         "orderDataType": "dom-checkbox"
                     }
                 ],
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index 65debd10..ae922389 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -14,9 +14,7 @@
         <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}">
         <input type="hidden" name="trait_id" value="{{ this_trait.name }}">
         <input type="hidden" name="dataset" value="{{ dataset.name }}">
-        {% if mapping_method == "reaper" or mapping_method == "rqtl_geno" %}
-        <input type="hidden" name="genofile" value="{{ dataset.group.genofile }}">
-        {% endif %}
+        <input type="hidden" name="genofile" value="{{ genofile_string }}">
         <input type="hidden" name="method" value="{{ mapping_method }}">
         {% for sample in samples %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
@@ -41,7 +39,10 @@
               {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.name }}</a><br>
               {% if dataset.type == "ProbeSet" %}
               <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br>
-              <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb
+              <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br>
+              {% endif %}
+              {% if genofile_string is defined %}
+              <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}
               {% endif %}
           </div>
           <div id="gn1_map_options" class="col-xs-5" style="outline: 3px double #AAAAAA; padding: 10px; margin: 10px;">
@@ -121,7 +122,7 @@
                     <span style="color:red;">*</span>
                   <br>
                   <input type="checkbox" name="showGenes" class="checkbox" style="display: inline; margin-top: 0px;" {% if geneChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Gene Track </span> <span style="color:red;">*</span><br>
-                  {% if plotScale != "morgan" and mapping_method != "gemma" %}
+                  {% if plotScale != "morgan" and mapping_method != "gemma" and mapping_method != "plink" %}
                   <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Analyst </span> <span style="color:red;">*</span><br>
                   {% endif %}
                   <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span>
@@ -234,7 +235,7 @@
           </table>
           </div>
         </div>
-        {% else %}
+        {% elif selectedChr != -1 and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %}
         <div>
           <h2>Interval Analyst</h2>
           <div id="table_container">
diff --git a/wqflask/wqflask/templates/network_graph.html b/wqflask/wqflask/templates/network_graph.html
index 50c0c230..24293de6 100644
--- a/wqflask/wqflask/templates/network_graph.html
+++ b/wqflask/wqflask/templates/network_graph.html
@@ -17,7 +17,7 @@
         <div class="row" >
           <div id="content">
             <div id="secondaryContent" class="col-xs-3">
-                <h3> Visualization Options</h3>
+                <h3 style="margin-top:0px; margin-bottom: 5px;"> Visualization Options</h3>
                 <table border="0">
                   <tbody>
                     <tr>
@@ -27,12 +27,13 @@
                     </tr>
                     <tr>
                       <td>
-                        Focus Trait
+                        Focus Trait<sup title="Only show edges connected to the specified node" style="color:#f00"> ?</sup>
                       </td>
                     </tr>
                     <tr>
                       <td>
                         <select name="focus_select">
+                          <option disabled selected value>Select Trait</option>
                           {% for trait in traits %}
                           <option value="{{ trait.name }}:{{ trait.dataset.name }}">{{ trait.symbol }} ({{ trait.name }})</option>
                           {% endfor %}
@@ -40,17 +41,15 @@
                       </td>
                     </tr>    
                     <tr>
-                      <td colspan="1">Correlation Coefficient</td>
-                    </tr>
-                    <tr>
-                      <td>
-                        <font size="2"><b>0 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-                                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
-                                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +/- 1</b></font>
+                      <td colspan="1">
+                         Correlation Coefficient<sup title="Filter edges to only show correlations less than the negative value specified with the slider and greater than the positive value. For example, moving the slider half way will display correlations less than -0.5 and greater than 0.5" style="color:#f00"> ?</sup>
                       </td>
                     </tr>
                     <tr>
-                      <td>
+                      <td colspan="1">
+                        <font size="2"><b>0 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+                                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
+                                            &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +/- 1</b></font><br>
                         <input type="range" id="slide" min="0" max="1" value="0" step="0.001" list="corr_range">
                       </td>
                     </tr>
@@ -73,7 +72,7 @@
                     </tr>                          
                   </tbody>
                 </table>    
-                <h3> Download</h3>
+                <h3 style="margin-bottom: 5px;"> Download</h3>
                 <table>
                   <tbody>
                     <tr>
@@ -86,7 +85,7 @@
                   </tbody>
                 </table>
             </div>
-            <div id="cytoscapeweb" class="col-xs-9" style="min-height:700px !important;"></div>
+            <div id="cytoscapeweb" class="col-xs-9" style="height:700px !important; border-style: solid; border-width: 1px; border-color: grey;"></div>
           </div>
         </div>
     </div>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 23c09d05..d8a18f38 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -44,7 +44,7 @@
                             <div style="margin-left: 20px;" class="col-xs-8 controls">
                                 <select id="genofile_reaper" class="form-control">
                                     {% for item in genofiles %}
-                                    <option value="{{item['location']}}">{{item['title']}}</option>
+                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                     {% endfor %}
                                 </select>
                             </div>
@@ -138,21 +138,12 @@
                             <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']}}</option>
+                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                     {% endfor %}
                                 </select>
                             </div>
                         </div>
                         {% endif %}
-                        <div class="mapping_method_fields form-group">
-                            <label 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_pylmm" value="" type="text" class="form-control">
-                            </div>
-                        </div>
-                        <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
-                            Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
-                        </div>
 <!--
                         <div class="mapping_method_fields form-group">
                             <label for="control_for" class="col-xs-3 control-label">Control&nbsp;for</label>
@@ -172,8 +163,6 @@
                                 </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">
@@ -187,6 +176,7 @@
                                </label>
                             </div>
                         </div>
+-->
                         <div class="form-group">
                             <div style="padding-left:15px;" class="controls">
                                 <button id="pylmm_compute" class="btn submit_special btn-primary" title="Compute Marker Regression">
@@ -205,7 +195,7 @@
                             <div style="margin-left: 20px;" class="col-xs-8 controls">
                                 <select id="genofile_rqtl_geno" class="form-control">
                                     {% for item in genofiles %}
-                                    <option value="{{item['location']}}">{{item['title']}}</option>
+                                    <option value="{{item['location']}}:{{item['title']}}">{{item['title']}}</option>
                                     {% endfor %}
                                 </select>
                             </div>
@@ -259,13 +249,13 @@
                             <div class="col-xs-4 controls">
                               <select name="mapmodel_rqtl_geno" class="form-control">
                                 <option value="normal">normal</option>
-                                <option value="binary">binary</option>
-                                <option value="2part">2part</option>
+                                <!--<option value="binary">binary</option>
+                                <option value="2part">2part</option>-->
                                 <option value="np">np</option>
                               </select>
                             </div>
                         </div>
-
+                        <!--
                         <div class="mapping_method_fields form-group">
                             <label style="text-align:left;" class="col-xs-12 control-label">Pair Scan</label>
                             <div class="col-xs-12 controls">
@@ -279,7 +269,7 @@
                                </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">