Replaced header with other information in qtl map

Began adding menu to qtl map

Fixed global search to not retrieve samples (to increase speed)

Got the vector plot working again so it can be displayed alongside the gn1-style plot

Only display the vector plot when doing GEMMA to speed up (this might not be necessary)

8 files changed, 163 insertions, 69 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 6cabadb1..e37a838f 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -54,7 +54,7 @@ from pprint import pformat as pf
 # Each subclass will add to this
 DS_NAME_MAP = {}
 
-def create_dataset(dataset_name, dataset_type = None):
+def create_dataset(dataset_name, dataset_type = None, get_samplelist = True):
     if not dataset_type:
         dataset_type = Dataset_Getter(dataset_name)
         #dataset_type = get_dataset_type_from_json(dataset_name)
@@ -71,7 +71,7 @@ def create_dataset(dataset_name, dataset_type = None):
 
     dataset_ob = DS_NAME_MAP[dataset_type]
     dataset_class = globals()[dataset_ob]
-    return dataset_class(dataset_name)
+    return dataset_class(dataset_name, get_samplelist)
 
 
 #def get_dataset_type_from_json(dataset_name):
@@ -501,7 +501,7 @@ class DataSet(object):
 
     """
 
-    def __init__(self, name):
+    def __init__(self, name, get_samplelist = True):
 
         assert name, "Need a name"
         self.name = name
@@ -517,7 +517,8 @@ class DataSet(object):
         self.retrieve_other_names()
         
         self.group = DatasetGroup(self)   # sets self.group and self.group_id and gets genotype
-        self.group.get_samplelist()
+        if get_samplelist == True:
+             self.group.get_samplelist()
         self.species = species.TheSpecies(self)
 
 
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index ff149ba3..acff38d9 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -67,7 +67,7 @@ class GeneralTrait(object):
         # Todo: These two lines are necessary most of the time, but perhaps not all of the time
         # So we could add a simple if statement to short-circuit this if necessary
         self.retrieve_info(get_qtl_info=get_qtl_info)
-        if kw.get('get_sample_info') != False:
+        if get_sample_info != False:
             self.retrieve_sample_data()
         
         
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index a6efb47f..4179dc48 100755
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -46,7 +46,7 @@ class GSearch(object):
 			self.trait_list = []
 			with Bench("Creating trait objects"):
 				for line in re:
-					dataset = create_dataset(line[3], "ProbeSet")
+					dataset = create_dataset(line[3], "ProbeSet", get_samplelist=False)
 					trait_id = line[4]
 					#with Bench("Building trait object"):
 					this_trait = GeneralTrait(dataset=dataset, name=trait_id, get_qtl_info=True, get_sample_info=False)
diff --git a/wqflask/wqflask/marker_regression/marker_regression_gn1.py b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
index 56286ee6..e9052290 100644
--- a/wqflask/wqflask/marker_regression/marker_regression_gn1.py
+++ b/wqflask/wqflask/marker_regression/marker_regression_gn1.py
@@ -295,10 +295,13 @@ class MarkerRegression(object):
         self.SNPChecked  = False
         self.draw2X = False
         self.lrsMax = 0
-        if 'mb_range' in start_vars:
-            self.startMb, self.endMb = [float(x) for x in start_vars['mb_range'].split(',')]
+        if 'startMb' in start_vars:
+            self.startMb = start_vars['startMb']
         else:
             self.startMb = -1
+        if 'endMb' in start_vars:
+            self.endMb = start_vars['endMb']
+        else:
             self.endMb = -1
 
         #self.additiveChecked = fd.formdata.getvalue('additiveCheck')
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
index 472ec12d..88003f4e 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.coffee
@@ -46,9 +46,5 @@ create_lod_chart = ->
                       .transition().duration(500).attr("r", r)
 
 $ ->
-    #window.setTimeout ( ->
-    #    console.log(js_data)
-    #), 1000
-    #window.setTimeout(create_lod_chart(), 1000)
     root.create_lod_chart = create_lod_chart
 
diff --git a/wqflask/wqflask/static/new/javascript/create_lodchart.js b/wqflask/wqflask/static/new/javascript/create_lodchart.js
index c756d842..778eed3a 100644
--- a/wqflask/wqflask/static/new/javascript/create_lodchart.js
+++ b/wqflask/wqflask/static/new/javascript/create_lodchart.js
@@ -1,45 +1,50 @@
-// Generated by CoffeeScript 1.9.2
-(function() {
-  var create_lod_chart;
+//var create_lod_chart;
 
-  create_lod_chart = function() {
-    var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
-    h = 500;
-    w = 1200;
-    margin = {
-      left: 60,
-      top: 40,
-      right: 40,
-      bottom: 40,
-      inner: 5
-    };
-    halfh = h + margin.top + margin.bottom;
-    totalh = halfh * 2;
-    totalw = w + margin.left + margin.right;
-    console.log("js_data:", js_data);
-    mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").mappingScale(js_data.mapping_scale).manhattanPlot(js_data.manhattan_plot);
-    data = js_data.json_data;
-    d3.select("div#topchart").datum(data).call(mychart);
-    chrrect = mychart.chrSelect();
-    chrrect.on("mouseover", function() {
-      return d3.select(this).attr("fill", "#E9CFEC");
-    }).on("mouseout", function(d, i) {
-      return d3.select(this).attr("fill", function() {
-        if (i % 2) {
-          return "#F1F1F9";
-        }
-        return "#FBFBFF";
-      });
-    });
-    return mychart.markerSelect().on("click", function(d) {
-      var r;
-      r = d3.select(this).attr("r");
-      return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
-    });
+create_lod_chart = function() {
+  var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w;
+  h = 500;
+  w = 1200;
+  margin = {
+    left: 60,
+    top: 40,
+    right: 40,
+    bottom: 40,
+    inner: 5
   };
-
-  $(function() {
-    return root.create_lod_chart = create_lod_chart;
+  halfh = h + margin.top + margin.bottom;
+  totalh = halfh * 2;
+  totalw = w + margin.left + margin.right;
+  if ('additive' in js_data) {
+    additive = js_data.additive;
+  } else {
+    additive = false;
+  }
+  console.log("js_data:", js_data);
+  mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot);
+  data = js_data.json_data;
+  d3.select("div#topchart").datum(data).call(mychart);
+  chrrect = mychart.chrSelect();
+  chrrect.on("mouseover", function() {
+    return d3.select(this).attr("fill", "#E9CFEC");
+  }).on("mouseout", function(d, i) {
+    return d3.select(this).attr("fill", function() {
+      if (i % 2) {
+        return "#F1F1F9";
+      }
+      return "#FBFBFF";
+    });
+  });
+  return mychart.markerSelect().on("click", function(d) {
+    var r;
+    r = d3.select(this).attr("r");
+    return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r);
   });
+};
+
+create_lod_chart()
 
-}).call(this);
+/*
+$(function() {
+  return root.create_lod_chart = create_lod_chart;
+});
+*/
\ No newline at end of file
diff --git a/wqflask/wqflask/templates/marker_regression_gn1.html b/wqflask/wqflask/templates/marker_regression_gn1.html
index dd8ae236..4eb5862a 100644
--- a/wqflask/wqflask/templates/marker_regression_gn1.html
+++ b/wqflask/wqflask/templates/marker_regression_gn1.html
@@ -3,22 +3,23 @@
 {% 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/new/css/marker_regression.css" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/panelutil.css" />
 {% endblock %}
 {% from "base_macro.html" import header %}
 {% block content %}
-    {{ header("Whole Genome Mapping Results",
-        '{}: {}'.format(this_trait.name, this_trait.description_fmt)) }}
-
     <div class="container">
         <form method="post" target="_blank" action="/marker_regression" name="marker_regression" id="marker_regression_form">
         <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 }}">
+        <input type="hidden" name="method" value="{{ mapping_method }}">
+        {% if mapping_method != "gemma" %}
         {% for sample in dataset.group.samplelist %}
         <input type="hidden" name="value:{{ sample }}" value="{{ vals[loop.index - 1] }}">
         {% endfor %}
         <input type="hidden" name="maf">
-        <input type="hidden" name="method" value="{{ mapping_method }}">
         <input type="hidden" name="selected_chr" value="{{ selectedChr }}">
         <input type="hidden" name="mb_range" value="{{ startMb|string + "," + endMb|string }}">
         <input type="hidden" name="manhattan_plot">
@@ -28,13 +29,80 @@
         <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}">
         <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}">
         <input type="hidden" name="pair_scan" value="{{ pair_scan }}">
-        <div id="chart_container">
-            <div class="qtlcharts" id="topchart">
-                {{ gifmap|safe }}
-                <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+        {% endif %}
+        
+        <div class="container">
+          <div class="col-xs-5">
+              <h2>Map Viewer: Whole Genome</h2><br>
+              <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br>
+              <b>Database:</b> {{ dataset.fullname }}<br>
+              {% 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
+              {% endif %}
+          </div>
+          {% if mapping_method != "gemma" %}
+          <div id="gn1_map_options" class="col-xs-5" style="border:2px solid black; padding: 10px; margin: 10px;">
+            <div class="col-xs-7" style="padding-left: 0px;">
+              <table>
+                <tr>
+                  <td><b>Chr:&nbsp;</b></td>
+                  <td>
+                    <select name="chromosomes" size="1">
+                        {% for chr in ChrList %}
+                        <option value="{{ chr[1] }}">{{ chr[0] }}</option>
+                        {% endfor %}
+                    </select>&nbsp;
+                    <button type="button" class="btn btn-primary">Remap</button>
+                  </td>
+                </tr>
+                <tr>
+                  <td><b>View:&nbsp;</b></td>
+                  <td>
+                    <input type="text" name="startMb"
+                  </td>
+                </tr>
+              </table>
+              </div>
+              <div class="col-xs-3">
+              </div>
+          </div>
+        </div>
+        {% endif %}
+        
+ 
+        <div class="tabbable" style="margin: 10px;">
+          <ul class="nav nav-tabs">
+            {% if mapping_method != "gemma" %}
+            <li id="gn1_map_tab">
+              <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a>
+            </li>
+            {% endif %}
+            <li id="vector_map_tab">
+              <a href="#vector_map" data-toggle="tab" {% if mapping_method != "gemma" %}aria-expanded="false"{% else %}aria-expanded="true"{% endif %}>Vector Map</a>
+            </li>
+          </ul>
+          <div class="tab-content">
+            {% if mapping_method != "gemma" %}
+            <div class="tab-pane active" id="gn1_map">
+              <div class="qtlcharts">
+                  {{ gifmap|safe }}
+                  <img src="/static/output/{{ filename }}.jpeg" usemap="#WebQTLImageMap">
+              </div>
             </div>
+            {% endif %}
+            <div class="tab-pane {% if mapping_method == "gemma" %}active{% endif %}" id="vector_map">
+              <div id="chart_container">
+                <div class="qtlcharts" id="topchart"></div>
+              </div>
+            </div>
+          </div>
         </div>
+
         </form>
+        
+        {% if mapping_method != "gemma" %} 
         <div style="width:48%;">
             <h2>
                 Results
@@ -87,6 +155,7 @@
                 </tbody>
             </table>
         </div>
+        {% endif %}
     </div>
 
     <!-- End of body -->
@@ -95,8 +164,10 @@
 
 {% block js %}  
 
+    <script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore-min.js"></script>
     <script type="text/javascript" src="/static/new/js_external/underscore.string.min.js"></script>
+    <script type="text/javascript" src="/static/new/js_external/d3-tip.min.js"></script>
 
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.js"></script>
     <script language="javascript" type="text/javascript" src="https://cdn.datatables.net/buttons/1.0.0/js/dataTables.buttons.min.js"></script>
@@ -111,6 +182,11 @@
         js_data = {{ js_data | safe }}
     </script>
 
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/panelutil.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/chr_lod_chart.js"></script> 
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/lod_chart.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/create_lodchart.js"></script>
+    
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
             console.time("Creating table");
@@ -137,7 +213,15 @@
             } );
             console.timeEnd("Creating table");
 
-        });
+            $('#vector_map_tab').click(function(){
+                $('div#gn1_map_options').hide();
+            });
+
+            $('#gn1_map_tab').click(function(){
+                $('div#gn1_map_options').show();
+            });
+
+            });
 
         chrView = function(this_chr, chr_mb_list) {
             $('input[name=selected_chr]').val(this_chr + 1)
@@ -148,10 +232,10 @@
 
         rangeView = function(this_chr, start_mb, end_mb) {
             $('input[name=selected_chr]').val(this_chr)
-            $('input[name=mb_range]').val(start_mb + "," + end_mb)
-            
-            console.log("mb_range:", $('input[name=mb_range]').val())
-            
+            $('input[name=startMb]').val(start_mb)
+            $('input[name=endMb]').val(end_mb)
+            //$('input[name=mb_range]').val(start_mb + "," + end_mb)
+
             return $('#marker_regression_form').submit();
         };
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 65b6dae4..17845826 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -352,7 +352,8 @@ def marker_regression_page():
         'control_marker_db',
         'do_control',
         'pair_scan',
-        'mb_range',
+        'startMb',
+        'endMb',
         'mapmethod_rqtl_geno',
         'mapmodel_rqtl_geno'
     )
@@ -391,7 +392,8 @@ def marker_regression_page():
         #for item in template_vars.__dict__.keys():
         #    print("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
         
-        gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
+        if start_vars['method'] != "gemma":
+            gn1_template_vars = marker_regression_gn1.MarkerRegression(result).__dict__
 
         #qtl_length = len(result['js_data']['qtl_results'])
         #print("qtl_length:", qtl_length)
@@ -414,7 +416,10 @@ def marker_regression_page():
             rendered_template = render_template("pair_scan_results.html", **result)
         else:
             #rendered_template = render_template("marker_regression.html", **result)
-            rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+            if start_vars['method'] != "gemma":
+                rendered_template = render_template("marker_regression_gn1.html", **gn1_template_vars)
+            else:
+                rendered_template = render_template("marker_regression_gn1.html", **result)
 
     return rendered_template