Fixed sorting on the show trait page

Added/improved the x and y axis on the bar graph and histogram

GEMMA working but still really slow

10 files changed, 270 insertions, 62 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 54cc9006..c220d2c9 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -58,6 +58,8 @@ class MarkerRegression(object):
  
         if self.mapping_method == "gemma":
             qtl_results = self.run_gemma()
+        elif self.mapping_method == "plink":
+            qtl_results = self.run_plink()
         elif self.mapping_method == "pylmm":
             #self.qtl_results = self.gen_data(tempdata)
             qtl_results = self.gen_data(str(temp_uuid))
@@ -151,6 +153,10 @@ class MarkerRegression(object):
     #
     #
     
+    def run_plink(self):
+    
+        os.chdir("/home/zas1024/plink")
+    
     #def gen_data(self, tempdata):
     def gen_data(self, temp_uuid):
         """Generates p-values for each marker"""
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index db8d4f1a..6f0ff44b 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -98,7 +98,10 @@ class ShowTrait(object):
         hddn['trait_id'] = self.trait_id
         hddn['dataset'] = self.dataset.name
         hddn['method'] = "pylmm"
-
+        hddn['mapping_display_all'] = True
+        hddn['suggestive'] = 0
+        hddn['maf'] = 0.01
+    
         # We'll need access to this_trait and hddn in the Jinja2 Template, so we put it inside self
         self.hddn = hddn
         
diff --git a/wqflask/wqflask/static/new/css/bar_chart.css b/wqflask/wqflask/static/new/css/bar_chart.css
index c8e081f9..3e6e7bd6 100755
--- a/wqflask/wqflask/static/new/css/bar_chart.css
+++ b/wqflask/wqflask/static/new/css/bar_chart.css
@@ -9,7 +9,7 @@
   fill: steelblue;

   shape-rendering: crispEdges;

 }

-

+/*

 .x.axis path {

   display: none;

-}
\ No newline at end of file
+}*/
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 6c1e65e9..98f89ac6 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -41,13 +41,15 @@ class Histogram
 

     create_x_scale: () ->

         console.log("min/max:", d3.min(@sample_vals) + "," + d3.max(@sample_vals))

-        if (d3.min(@sample_vals) < 0)

-            min_domain = d3.min(@sample_vals)

-        else

-            min_domain = 0

+        x0 = Math.max(-d3.min(@sample_vals), d3.max(@sample_vals))

+        #if (d3.min(@sample_vals) < 0)

+        #    min_domain = d3.min(@sample_vals)

+        #else

+        #    min_domain = 0

         @x_scale = d3.scale.linear()

-            .domain([min_domain, parseFloat(d3.max(@sample_vals))])

-            .range([0, @plot_width]) 

+            .domain([d3.min(@sample_vals), d3.max(@sample_vals)])

+            .range([0, @plot_width])

+            .nice()

 

     get_histogram_data: () ->

         console.log("sample_vals:", @sample_vals)

@@ -62,6 +64,7 @@ class Histogram
 

     create_graph: () ->

         @add_x_axis()

+        @add_y_axis()

         @add_bars()

 

     add_x_axis: () ->

@@ -74,11 +77,32 @@ class Histogram
             .attr("transform", "translate(0," + @plot_height + ")")

             .call(x_axis)

             

+    #add_y_axis: () ->

+    #    y_axis = d3.svg.axis()

+    #            .scale(@y_scale)

+    #            .orient("left")

+    #            .ticks(5)

+    #            

+    #    @svg.append("g")

+    #        .attr("class", "y axis")

+    #        #.attr("transform", "translate(0," + @plot_width + ")")

+    #        .call(y_axis)

+            

+            

     add_y_axis: () ->

-        y_axis = d3.svg.axis()

+        yAxis = d3.svg.axis()

                 .scale(@y_scale)

                 .orient("left")

                 .ticks(5)

+

+        @svg.append("g")

+            .attr("class", "y axis")

+            .call(yAxis)

+          .append("text")

+            .attr("transform", "rotate(-90)")

+            .attr("y", 6)

+            .attr("dy", ".71em")

+            .style("text-anchor", "end")

                 

     add_bars: () ->

         console.log("bar_width:", @x_scale(@histogram_data[0].dx))

diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index 1603cb77..d8067ced 100755
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -55,14 +55,10 @@
     };
 
     Histogram.prototype.create_x_scale = function() {
-      var min_domain;
+      var x0;
       console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals));
-      if (d3.min(this.sample_vals) < 0) {
-        min_domain = d3.min(this.sample_vals);
-      } else {
-        min_domain = 0;
-      }
-      return this.x_scale = d3.scale.linear().domain([min_domain, parseFloat(d3.max(this.sample_vals))]).range([0, this.plot_width]);
+      x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals));
+      return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice();
     };
 
     Histogram.prototype.get_histogram_data = function() {
@@ -82,6 +78,7 @@
 
     Histogram.prototype.create_graph = function() {
       this.add_x_axis();
+      this.add_y_axis();
       return this.add_bars();
     };
 
@@ -92,8 +89,9 @@
     };
 
     Histogram.prototype.add_y_axis = function() {
-      var y_axis;
-      return y_axis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+      var yAxis;
+      yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+      return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end");
     };
 
     Histogram.prototype.add_bars = function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index 84e465e8..a410baf3 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -204,6 +204,7 @@ $ ->
                 name = $.trim(name)
                 real_value = $(row).find('.edit_sample_value').val()
                 console.log("real_value:", real_value)
+                
                 checkbox = $(row).find(".edit_sample_checkbox")
                 checked = $(checkbox).attr('checked')
 
diff --git a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
index f1024cd1..1d375686 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.coffee
@@ -56,6 +56,9 @@ $ ->
         console.log("In interval mapping")
         $("#progress_bar_container").modal()
         url = "/interval_mapping"
+        $('input[name=method]').val("reaper")
+        $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'))
+        $('input[name=suggestive]').val($('input[name=suggestive_reaper]'))
         form_data = $('#trait_data_form').serialize()
         console.log("form_data is:", form_data)
         $.ajax(
@@ -116,9 +119,41 @@ $ ->
         return false
     )
 
+    $("#plink_compute").click(() =>
+        url = "/marker_regression"
+        $('input[name=method]').val("plink")
+        $('input[name=mapping_display_all]').val($('input[name=display_all_plink]'))
+        $('input[name=suggestive]').val($('input[name=suggestive_plink]'))
+        $('input[name=maf]').val($('input[name=maf_plink]'))
+        form_data = $('#trait_data_form').serialize()
+        console.log("form_data is:", form_data)
+        $.ajax(
+            type: "POST"
+            url: url
+            data: form_data
+            error: (xhr, ajaxOptions, thrownError) =>
+                alert("Sorry, an error occurred")
+                console.log(xhr)
+                clearInterval(this.my_timer)
+                $('#progress_bar_container').modal('hide')
+                $("body").html("We got an error.")        
+            success: (data) =>
+                clearInterval(this.my_timer)
+                $('#progress_bar_container').modal('hide')
+                $("body").html(data)
+        )
+        console.log("settingInterval")
+
+        this.my_timer = setInterval(get_progress, 1000)
+        return false
+    )
+
     $("#gemma_compute").click(() =>
         url = "/marker_regression"
         $('input[name=method]').val("gemma")
+        $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]'))
+        $('input[name=suggestive]').val($('input[name=suggestive_gemma]'))
+        $('input[name=maf]').val($('input[name=maf_gemma]'))
         form_data = $('#trait_data_form').serialize()
         console.log("form_data is:", form_data)
         $.ajax(
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 a5a49ace..dbc26e3b 100755
--- a/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait_mapping_tools.js
@@ -67,6 +67,9 @@
       console.log("In interval mapping");
       $("#progress_bar_container").modal();
       url = "/interval_mapping";
+      $('input[name=method]').val("reaper");
+      $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_reaper]'));
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
       $.ajax({
@@ -127,10 +130,43 @@
       _this.my_timer = setInterval(get_progress, 1000);
       return false;
     });
+    $("#plink_compute").click(function() {
+      var form_data, url;
+      url = "/marker_regression";
+      $('input[name=method]').val("plink");
+      $('input[name=mapping_display_all]').val($('input[name=display_all_plink]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_plink]'));
+      $('input[name=maf]').val($('input[name=maf_plink]'));
+      form_data = $('#trait_data_form').serialize();
+      console.log("form_data is:", form_data);
+      $.ajax({
+        type: "POST",
+        url: url,
+        data: form_data,
+        error: function(xhr, ajaxOptions, thrownError) {
+          alert("Sorry, an error occurred");
+          console.log(xhr);
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          return $("body").html("We got an error.");
+        },
+        success: function(data) {
+          clearInterval(_this.my_timer);
+          $('#progress_bar_container').modal('hide');
+          return $("body").html(data);
+        }
+      });
+      console.log("settingInterval");
+      _this.my_timer = setInterval(get_progress, 1000);
+      return false;
+    });
     $("#gemma_compute").click(function() {
       var form_data, url;
       url = "/marker_regression";
       $('input[name=method]').val("gemma");
+      $('input[name=mapping_display_all]').val($('input[name=display_all_gemma]'));
+      $('input[name=suggestive]').val($('input[name=suggestive_gemma]'));
+      $('input[name=maf]').val($('input[name=maf_gemma]'));
       form_data = $('#trait_data_form').serialize();
       console.log("form_data is:", form_data);
       $.ajax({
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index e15d043b..ff05e859 100755
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -69,38 +69,98 @@
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.naturalSort.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/DT_bootstrap/DT_bootstrap.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
+        <script type="text/javascript" charset="utf-8">
+            
+           function getValue(x) {
+                if (x.indexOf('input') >= 0) {
+                    if ($(x).val() == 'x') {
+                        return 0
+                    }
+                    else {
+                       return parseFloat($(x).val());
+                    }
+                }
+                return parseFloat(x);
+            }
+            
+            jQuery.fn.dataTableExt.oSort['cust-txt-asc'] = function (a, b) {
+                var x = getValue(a);
+                var y = getValue(b);
+                return ((x < y) ? -1 : ((x > y) ? 1 : 0));
+            };
+            
+            jQuery.fn.dataTableExt.oSort['cust-txt-desc'] = function (a, b) {
+                var x = getValue(a);
+                var y = getValue(b);
+                return ((x < y) ? 1 : ((x > y) ? -1 : 0));
+            };
+            
+            $(document).ready( function () {
+                console.time("Creating table");
+                
+                {% if sample_groups[0].se_exists() %}
+                    $('#samples_primary, #samples_other').dataTable( {
+                        //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+                        "aoColumns": [
+                            { "sType": "natural" },
+                            null,
+                            { "sType": "cust-txt" },
+                            { "bSortable": false },
+                            { "sType": "cust-txt" }
+                        ],
+                        "sDom": "ftr",
+                        "oTableTools": {
+                            "aButtons": [
+                                "copy",
+                                "print",
+                                {
+                                    "sExtends":    "collection",
+                                    "sButtonText": 'Save <span class="caret" />',
+                                    "aButtons":    [ "csv", "xls", "pdf" ]
+                                }
+                            ],
+                            "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+                        },
+                        "bPaginate": false,
+                        "bLengthChange": true,
+                        "bDeferRender": true,
+                        "bSortClasses": false
+                    } );
+                    console.timeEnd("Creating table");
+
+                {% else %}
+        
+            
+                    console.time("Creating table");
+                    
+                    $('#samples_primary, #samples_other').dataTable( {
+                        //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
+                        "aoColumns": [
+                            { "sType": "natural" },
+                            null,
+                            { "sType": "cust-txt" }
+                        ],
+                        "sDom": "ftr",
+                        "oTableTools": {
+                            "aButtons": [
+                                "copy",
+                                "print",
+                                {
+                                    "sExtends":    "collection",
+                                    "sButtonText": 'Save <span class="caret" />',
+                                    "aButtons":    [ "csv", "xls", "pdf" ]
+                                }
+                            ],
+                            "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
+                        },
+                        "bPaginate": false,
+                        "bLengthChange": true,
+                        "bDeferRender": true,
+                        "bSortClasses": false
+                    } );
+                    console.timeEnd("Creating table");
+                {% endif %}
+            });
+        </script>
     
-    <script type="text/javascript" charset="utf-8">
-        $(document).ready( function () {
-            console.time("Creating table");
-            $('#samples_primary, #samples_other').dataTable( {
-                //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
-                "aoColumns": [
-                    { "sType": "natural" },
-                    null,
-                    null,
-                    { "bSortable": false },
-                    null
-                ],
-                "sDom": "ftr",
-                "oTableTools": {
-                    "aButtons": [
-                        "copy",
-                        "print",
-                        {
-                            "sExtends":    "collection",
-                            "sButtonText": 'Save <span class="caret" />',
-                            "aButtons":    [ "csv", "xls", "pdf" ]
-                        }
-                    ],
-                    "sSwfPath": "/static/packages/TableTools/media/swf/copy_csv_xls_pdf.swf"
-                },
-                "bPaginate": false,
-                "bLengthChange": true,
-                "bDeferRender": true,
-                "bSortClasses": false
-            } );
-            console.timeEnd("Creating table");
-        });
-    </script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index cc995f2f..f380988e 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -10,6 +10,9 @@
                     <a href="#marker_regression" data-toggle="tab">Marker Regression</a>
                 </li>
                 <li>
+                    <a href="#plink" data-toggle="tab">PLINK</a>
+                </li>
+                <li>
                     <a href="#gemma" data-toggle="tab">GEMMA</a>
                 </li>
                 <!--<li>
@@ -114,20 +117,20 @@
                         <label class="control-label">Display all</label>
                         <div class="controls">                      
                             <label class="radio inline">
-                                <input type="radio" name="display_all" value="True" checked>
+                                <input type="radio" name="display_all_reaper" value="True" checked>
                                 Yes
                             </label>
                             <label class="radio inline">
-                                <input type="radio" name="display_all" value="False">
+                                <input type="radio" name="display_all_reaper" value="False">
                                 No
                             </label>
                         </div>
                     </div>
                     <div class="control-group" id="suggestive" >
-                        <label for="suggestive" class="control-label"
+                        <label for="suggestive_reaper" class="control-label"
                                title="Control Locus">LOD score greater than: </label>
                         <div class="controls">
-                            <input name="suggestive" type="text" value="0"/>
+                            <input name="suggestive_reaper" type="text" value="0"/>
                         </div>
                     </div>
                     
@@ -151,32 +154,74 @@
                     
                 </div>
                 
+                <div class="tab-pane" id="plink">
+                    <div class="control-group" id="display_all_div">
+                        <label class="control-label">Display all</label>
+                        <div class="controls">                      
+                            <label class="radio inline">
+                                <input type="radio" name="display_all_plink" value="True" checked>
+                                Yes
+                            </label>
+                            <label class="radio inline">
+                                <input type="radio" name="display_all_plink" value="False">
+                                No
+                            </label>
+                        </div>
+                    </div>
+                    <div class="control-group" id="suggestive" >
+                        <label for="suggestive_plink" class="control-label"
+                               title="Control Locus">LOD score greater than: </label>
+                        <div class="controls">
+                            <input name="suggestive_plink" type="text" value="0"/>
+                        </div>
+                    </div>
+                    <div class="control-group" id="suggestive" >
+                        <label for="maf_plink" class="control-label"
+                               title="Control Locus">Minor allele threshold: </label>
+                        <div class="controls">
+                            <input name="maf_plink" type="text" value="0.01"/>
+                        </div>
+                    </div>
+                    
+                    <div class="control-group">
+                        <div class="controls">
+                            <button id="plink_compute"
+                                    class="btn btn-inverse submit_special"
+                                    data-url="/marker_regression"
+                                    title="Compute using PLINK">
+                                <i class="icon-ok-circle icon-white"></i> Compute
+                            </button>
+                        </div>
+                    </div>
+                    
+                </div>
+                
                 <div class="tab-pane" id="gemma">
                     <div class="control-group" id="display_all_div">
                         <label class="control-label">Display all</label>
                         <div class="controls">                      
                             <label class="radio inline">
-                                <input type="radio" name="display_all" value="True" checked>
+                                <input type="radio" name="display_all_gemma" value="True" checked>
                                 Yes
                             </label>
                             <label class="radio inline">
-                                <input type="radio" name="display_all" value="False">
+                                <input type="radio" name="display_all_gemma" value="False">
                                 No
                             </label>
                         </div>
                     </div>
                     <div class="control-group" id="suggestive" >
-                        <label for="suggestive" class="control-label"
+                        <label for="suggestive_gemma" class="control-label"
                                title="Control Locus">LOD score greater than: </label>
                         <div class="controls">
-                            <input name="suggestive" type="text" value="0"/>
+                            <input name="suggestive_gemma" type="text" value="0"/>
                         </div>
                     </div>
                     <div class="control-group" id="suggestive" >
-                        <label for="maf" class="control-label"
+                        <label for="maf_gemma" class="control-label"
                                title="Control Locus">Minor allele threshold: </label>
                         <div class="controls">
-                            <input name="maf" type="text" value="0.01"/>
+                            <input name="maf_gemma" type="text" value="0.01"/>
                         </div>
                     </div>