Limited number of markers in marker regression result table to

those with a lod score > 2

Did some work towards adding the colored backgrounds to chromosome
areas in the manhattan plot

Changed the last two chromosomes for human manhattan plots to
X and X/Y

Started work on writing a script that can independently run the
pyLMM code and store the results in redis

10 files changed, 127 insertions, 41 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 0d295bed..9fbccf80 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -169,7 +169,6 @@ class Markers(object):
         for marker, p_value in itertools.izip(self.markers, p_values):
             marker['p_value'] = p_value
             if math.isnan(marker['p_value']) or marker['p_value'] <= 0:
-                print("p_value is:", marker['p_value'])
                 marker['lod_score'] = 0
                 marker['lrs_value'] = 0
             else:
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index fa9e0b67..5fa288df 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -158,6 +158,11 @@ def create_snp_iterator_file(group):
     with gzip.open(snp_file_base, "wb") as fh:
         pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL)
 
+#if __name__ == '__main__':
+#    import cPickle as pickle
+#    import gzip
+#    create_snp_iterator_file("HLC")
+    
 if __name__ == '__main__':
     import cPickle as pickle
     import gzip
diff --git a/wqflask/wqflask/my_pylmm/run_pylmm.py b/wqflask/wqflask/my_pylmm/run_pylmm.py
index 9ac03ad2..0c96d986 100644
--- a/wqflask/wqflask/my_pylmm/run_pylmm.py
+++ b/wqflask/wqflask/my_pylmm/run_pylmm.py
@@ -28,7 +28,7 @@ from base.species import TheSpecies
         if dataset.group.species == "human":

             p_values, t_stats = gen_human_results(pheno_vector, tempdata)

         else:

-            genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]

+            genotype_data = [marker['genotypes'] for marker in dataset.group.markers.markers]

             

             no_val_samples = self.identify_empty_samples()

             trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)

diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 93d3b5de..2063e638 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -14,7 +14,7 @@ $ ->
             @marker_names = []
             console.time('Create coordinates')
             @create_coordinates()
-            #console.log("@x_coords: ", @x_coords)
+            console.log("@x_coords: ", @x_coords)
             console.log("@y_coords: ", @y_coords)
             console.timeEnd('Create coordinates')
             [@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths()
@@ -85,8 +85,10 @@ $ ->
                 if not(result.chr in chr_seen)
                     chr_seen.push(result.chr) 
                     chr_lengths.push(chr_length)
-                    #console.log("result.chr:", result.chr)
+                    console.log("result.chr:", result.chr)
+                    console.log("total_length:", @total_length)
                     if result.chr != 1
+                        console.log("plus:", chr_lengths.length - 2)
                         @total_length += parseFloat(chr_lengths[chr_lengths.length - 2])
                 #console.log("total_length3:", @total_length)
                 #console.log("Mb:", result.Mb)
@@ -120,7 +122,7 @@ $ ->
             @add_x_axis()
             @add_y_axis()
             @add_chr_lines()
-            @fill_chr_areas()
+            #@fill_chr_areas()
             @add_chr_labels()
             @add_plot_points()
 
@@ -152,14 +154,18 @@ $ ->
             #@x_scale = d3.scale.linear()
             #    .domain([0, d3.max(@x_coords)])
             #    .range([@x_buffer, @plot_width])
-            console.log("@chromosomes[24]:", @chromosomes['24'])
-            console.log("@chromosomes[23]:", @chromosomes['23'])
-            console.log("@total_length:", @total_length)
-            console.log("d3.max(@xcoords):", d3.max(@x_coords))
-            @x_scale = d3.scale.linear()
-                .domain([0, (@total_length + @chromosomes['24'])])
-                .range([@x_buffer, @plot_width])
-
+            if '24' of @chromosomes
+                console.log("@chromosomes[24]:", @chromosomes['24'])
+                console.log("@chromosomes[23]:", @chromosomes['23'])
+                console.log("@total_length:", @total_length)
+                console.log("d3.max(@xcoords):", d3.max(@x_coords))
+                @x_scale = d3.scale.linear()
+                    .domain([0, (@total_length + @chromosomes['24'])])
+                    .range([@x_buffer, @plot_width])
+            else
+                @x_scale = d3.scale.linear()
+                    .domain([0, (@total_length + @chromosomes['20'])])
+                    .range([@x_buffer, @plot_width])
             @y_scale = d3.scale.linear()
                 .domain([2, @y_max])
                 .range([@plot_height, @y_buffer])
@@ -244,26 +250,61 @@ $ ->
                 .attr("y2", @plot_height)
                 .style("stroke", "#ccc")
                 
+                
         fill_chr_areas: () ->
+            console.log("cumu_chr_lengths:", @cumulative_chr_lengths)
+            console.log("example:", @x_scale(@cumulative_chr_lengths[0]))
+            @svg.selectAll("rect.chr_fill_area")
+                .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) =>
+                    return d
+                )
+                .enter()
+                .append("rect")
+                .attr("x", (d) =>
+                    if i == 0
+                        return @x_scale(0)
+                    else
+                        return @x_scale(d[1])
+                )
+                .attr("y", @y_buffer)
+                .attr("width", (d) =>
+                    return @x_scale(d[0])
+                )
+                .attr("height", @plot_height-@y_buffer)
+                #.attr("fill", (d, i) =>
+                #    if i%2
+                #        return "whitesmoke"
+                #    else
+                #        return "none"
+                #)
+                
+        fill_chr_areas2: () ->
+            console.log("cumu_chr_lengths:", @cumulative_chr_lengths)
+            console.log("example:", @x_scale(@cumulative_chr_lengths[0]))
             @svg.selectAll("rect.chr_fill_area")
                 .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) =>
                     return d
                 )
                 .enter()
                 .append("rect")
-                .attr("class", "chr_fill_area")
-                .attr("x", (d, i) =>
+                .attr("x", (d) =>
                     if i == 0
                         return @x_scale(0)
                     else
-                        return @x_scale(@cumulative_chr_lengths[i-1])
+                        return @x_scale(d[1])
                 )
                 .attr("y", @y_buffer)
                 .attr("width", (d) =>
                     return @x_scale(d[0])
                 )
                 .attr("height", @plot_height-@y_buffer)
-                .attr("fill", "none")
+                .attr("fill", (d, i) =>
+                    return "whitesmoke"
+                    #if i%2
+                    #    return "whitesmoke"
+                    #else
+                    #    return "none"
+                )
 
         add_chr_labels: () ->
             chr_names = []
@@ -277,7 +318,12 @@ $ ->
                 .enter()
                 .append("text")
                 .text((d) =>
-                    return d[0]
+                    if d[0] == "23"
+                        return "X"
+                    else if d[0] == "24"
+                        return "X/Y"
+                    else
+                        return d[0]
                 )
                 .attr("x", (d) =>
                     return @x_scale(d[2] - d[1]/2)
@@ -287,7 +333,7 @@ $ ->
                 .attr("text-anchor", "middle")
                 .attr("font-family", "sans-serif")
                 .attr("font-size", "18px")
-                .attr("fill", "grey")
+                .attr("fill", "black")
 
         add_plot_points: () ->
             @svg.selectAll("circle")
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 8e5b6c11..af6e0dbe 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -20,6 +20,7 @@
         this.marker_names = [];
         console.time('Create coordinates');
         this.create_coordinates();
+        console.log("@x_coords: ", this.x_coords);
         console.log("@y_coords: ", this.y_coords);
         console.timeEnd('Create coordinates');
         _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
@@ -93,7 +94,10 @@
           if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
             chr_seen.push(result.chr);
             chr_lengths.push(chr_length);
+            console.log("result.chr:", result.chr);
+            console.log("total_length:", this.total_length);
             if (result.chr !== 1) {
+              console.log("plus:", chr_lengths.length - 2);
               this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
             }
           }
@@ -131,7 +135,6 @@
         this.add_x_axis();
         this.add_y_axis();
         this.add_chr_lines();
-        this.fill_chr_areas();
         this.add_chr_labels();
         return this.add_plot_points();
       };
@@ -152,11 +155,15 @@
       };
 
       Manhattan_Plot.prototype.create_scales = function() {
-        console.log("@chromosomes[24]:", this.chromosomes['24']);
-        console.log("@chromosomes[23]:", this.chromosomes['23']);
-        console.log("@total_length:", this.total_length);
-        console.log("d3.max(@xcoords):", d3.max(this.x_coords));
-        this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['24']]).range([this.x_buffer, this.plot_width]);
+        if ('24' in this.chromosomes) {
+          console.log("@chromosomes[24]:", this.chromosomes['24']);
+          console.log("@chromosomes[23]:", this.chromosomes['23']);
+          console.log("@total_length:", this.total_length);
+          console.log("d3.max(@xcoords):", d3.max(this.x_coords));
+          this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['24']]).range([this.x_buffer, this.plot_width]);
+        } else {
+          this.x_scale = d3.scale.linear().domain([0, this.total_length + this.chromosomes['20']]).range([this.x_buffer, this.plot_width]);
+        }
         return this.y_scale = d3.scale.linear().domain([2, this.y_max]).range([this.plot_height, this.y_buffer]);
       };
 
@@ -230,17 +237,38 @@
 
       Manhattan_Plot.prototype.fill_chr_areas = function() {
         var _this = this;
+        console.log("cumu_chr_lengths:", this.cumulative_chr_lengths);
+        console.log("example:", this.x_scale(this.cumulative_chr_lengths[0]));
         return this.svg.selectAll("rect.chr_fill_area").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
           return d;
-        }).enter().append("rect").attr("class", "chr_fill_area").attr("x", function(d, i) {
+        }).enter().append("rect").attr("x", function(d) {
           if (i === 0) {
             return _this.x_scale(0);
           } else {
-            return _this.x_scale(_this.cumulative_chr_lengths[i - 1]);
+            return _this.x_scale(d[1]);
           }
         }).attr("y", this.y_buffer).attr("width", function(d) {
           return _this.x_scale(d[0]);
-        }).attr("height", this.plot_height - this.y_buffer).attr("fill", "none");
+        }).attr("height", this.plot_height - this.y_buffer);
+      };
+
+      Manhattan_Plot.prototype.fill_chr_areas2 = function() {
+        var _this = this;
+        console.log("cumu_chr_lengths:", this.cumulative_chr_lengths);
+        console.log("example:", this.x_scale(this.cumulative_chr_lengths[0]));
+        return this.svg.selectAll("rect.chr_fill_area").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+          return d;
+        }).enter().append("rect").attr("x", function(d) {
+          if (i === 0) {
+            return _this.x_scale(0);
+          } else {
+            return _this.x_scale(d[1]);
+          }
+        }).attr("y", this.y_buffer).attr("width", function(d) {
+          return _this.x_scale(d[0]);
+        }).attr("height", this.plot_height - this.y_buffer).attr("fill", function(d, i) {
+          return "whitesmoke";
+        });
       };
 
       Manhattan_Plot.prototype.add_chr_labels = function() {
@@ -254,10 +282,16 @@
         return this.svg.selectAll("text").data(chr_info, function(d) {
           return d;
         }).enter().append("text").text(function(d) {
-          return d[0];
+          if (d[0] === "23") {
+            return "X";
+          } else if (d[0] === "24") {
+            return "X/Y";
+          } else {
+            return d[0];
+          }
         }).attr("x", function(d) {
           return _this.x_scale(d[2] - d[1] / 2);
-        }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "grey");
+        }).attr("y", this.plot_height * 0.1).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black");
       };
 
       Manhattan_Plot.prototype.add_plot_points = function() {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index e45bb0be..84e465e8 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -125,6 +125,7 @@ $ ->
         console.log("*-* the_value:", the_value)
         console.log("*-* current_value:", current_value)
         if the_value != current_value
+            console.log("object:", $(id).html(the_value))
             $(id).html(the_value).effect("highlight")
 
         # We go ahead and always change the title value if we have it
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index c28b05f5..d4e01e6d 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -123,6 +123,7 @@
       console.log("*-* the_value:", the_value);
       console.log("*-* current_value:", current_value);
       if (the_value !== current_value) {
+        console.log("object:", $(id).html(the_value));
         $(id).html(the_value).effect("highlight");
       }
       if (title_value) {
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index c1d4d7e5..61a18e66 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -39,13 +39,15 @@
             </thead>
             <tbody>
                 {% for marker in qtl_results %}
-                <tr>
-                    <td>{{loop.index}}</td>
-                    <td>{{marker.lod_score}}</td>
-                    <td>{{marker.chr}}</td>
-                    <td>{{marker.Mb}}</td>
-                    <td>{{marker.name}}</td>
-                </tr>
+                    {% if marker.lod_score > 2 %}
+                    <tr>
+                        <td>{{loop.index}}</td>
+                        <td>{{marker.lod_score}}</td>
+                        <td>{{marker.chr}}</td>
+                        <td>{{marker.Mb}}</td>
+                        <td>{{marker.name}}</td>
+                    </tr>
+                    {% endif %}
                 {% endfor %}
             </tbody>
         </table>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 8822fd00..e15d043b 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -65,9 +65,7 @@
     <script type="text/javascript" src="/static/new/javascript/show_trait.js"></script>
     <script type="text/javascript" src="/static/new/javascript/validation.js"></script>
     
-<!--    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/dataTables.formattedNumbers.js"></script>
     <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>
@@ -104,5 +102,5 @@
             } );
             console.timeEnd("Creating table");
         });
-    </script>-->
+    </script>
 {% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 58ee8982..cfa49456 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -133,7 +133,7 @@
                         <div class="controls">
                             <input name="num_perm" value="2000" type="text" />
                         </div>
-                    </div>           -->         
+                    </div>           -->
                     
                     <div class="control-group">
                         <div class="controls">