From 6b367e3e2ee144aae5b79c50234faf0ea49adba6 Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 23 Jan 2014 21:52:03 +0000
Subject: Histogram is working

Fixed some bug with generating the manhattan plot for the HLC data set
---
 wqflask/base/data_set.py                           |   2 +
 .../wqflask/marker_regression/marker_regression.py |  11 +-
 wqflask/wqflask/my_pylmm/data/genofile_parser.py   |   6 +-
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py              |   2 +-
 .../wqflask/static/new/javascript/histogram.coffee |  96 ++++-----------
 wqflask/wqflask/static/new/javascript/histogram.js |  72 ++++-------
 .../static/new/javascript/marker_regression.coffee |  42 +++++--
 .../static/new/javascript/marker_regression.js     |  30 +++--
 .../static/new/javascript/show_trait.coffee        |   3 +-
 .../wqflask/static/new/javascript/show_trait.js    |   1 -
 wqflask/wqflask/templates/marker_regression.html   |   3 +-
 wqflask/wqflask/templates/show_trait.html          |  41 +++++++
 .../wqflask/templates/show_trait_edit_data.html    | 132 ++++++++++-----------
 wqflask/wqflask/views.py                           |   7 +-
 14 files changed, 226 insertions(+), 222 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d421f21e..0d295bed 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -185,6 +185,7 @@ class HumanMarkers(Markers):
         self.markers = []
         for line in marker_data_fh:
             splat = line.strip().split()
+            print("splat:", splat)
             marker = {}
             marker['chr'] = int(splat[0])
             marker['name'] = splat[1]
@@ -204,6 +205,7 @@ class HumanMarkers(Markers):
         #    #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
         #    marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
         
+        print("p_values2:", p_values)
         super(HumanMarkers, self).add_pvalues(p_values)
         
         with Bench("deleting markers"):
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 006c586b..fa9e0b67 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -48,7 +48,7 @@ class MarkerRegression(object):
             self.samples.append(str(sample))
             self.vals.append(value)
  
-        self.gen_data(tempdata)
+        self.qtl_results = self.gen_data(tempdata)
 
         #Get chromosome lengths for drawing the manhattan plot
         chromosome_mb_lengths = {}
@@ -78,9 +78,9 @@ class MarkerRegression(object):
             
             genotype_matrix = np.array(trimmed_genotype_data).T
             
-            print("pheno_vector: ", pf(pheno_vector))
-            print("genotype_matrix: ", pf(genotype_matrix))
-            print("genotype_matrix.shape: ", pf(genotype_matrix.shape))
+            #print("pheno_vector: ", pf(pheno_vector))
+            #print("genotype_matrix: ", pf(genotype_matrix))
+            #print("genotype_matrix.shape: ", pf(genotype_matrix.shape))
             
             t_stats, p_values = lmm.run(
                 pheno_vector,
@@ -89,9 +89,10 @@ class MarkerRegression(object):
                 refit=False,
                 temp_data=tempdata
             )
+            #print("p_values:", p_values)
         
         self.dataset.group.markers.add_pvalues(p_values)
-        self.qtl_results = self.dataset.group.markers.markers
+        return self.dataset.group.markers.markers
 
 
     def gen_human_results(self, pheno_vector, tempdata):
diff --git a/wqflask/wqflask/my_pylmm/data/genofile_parser.py b/wqflask/wqflask/my_pylmm/data/genofile_parser.py
index c8c0929f..4ebadb6e 100644
--- a/wqflask/wqflask/my_pylmm/data/genofile_parser.py
+++ b/wqflask/wqflask/my_pylmm/data/genofile_parser.py
@@ -106,7 +106,7 @@ class ConvertGenoFile(object):
                     this_marker.genotypes.append("NA")
                 
             #print("this_marker is:", pf(this_marker.__dict__))   
-            if this_marker.chr == "5":
+            if this_marker.chr == "14":
                 self.markers.append(this_marker.__dict__)
 
         with open(self.output_file, 'w') as fh:
@@ -125,8 +125,8 @@ class ConvertGenoFile(object):
 
     def process_rows(self):
         for self.latest_row_pos, row in enumerate(self.input_fh):
-            if self.input_file.endswith(".geno.gz"):
-                print("row: ", row)
+            #if self.input_file.endswith(".geno.gz"):
+            #    print("row: ", row)
             self.latest_row_value = row
             # Take care of headers
             if not row.strip():
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 60d36b8d..6d12991f 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -136,7 +136,7 @@ def run_human(pheno_vector,
         #print("***** Added to {} queue *****".format(key))
         for snp, this_id in plink_input:
             #with Bench("part before association"):
-            #if count > 2000:
+            #if count > 1000:
             #    break
             count += 1
 
diff --git a/wqflask/wqflask/static/new/javascript/histogram.coffee b/wqflask/wqflask/static/new/javascript/histogram.coffee
index 03332835..f1799307 100644
--- a/wqflask/wqflask/static/new/javascript/histogram.coffee
+++ b/wqflask/wqflask/static/new/javascript/histogram.coffee
@@ -4,10 +4,7 @@ class Histogram
     constructor: (@sample_list, @sample_group) ->
         @sort_by = "name"
         @format_count = d3.format(",.0f") #a formatter for counts
-        @get_samples()
-        #if @sample_attr_vals.length > 0
-        #    @get_distinct_attr_vals()
-        #    @get_attr_color_dict(@distinct_attr_vals)
+        @get_sample_vals()
         
         @margin = {top: 10, right: 30, bottom: 30, left: 30}
         @plot_width = 960 - @margin.left - @margin.right
@@ -28,21 +25,9 @@ class Histogram
 
         @create_graph()
 
-    get_samples: () ->
-        @sample_names = (sample.name for sample in @sample_list when sample.value != null)
+    get_sample_vals: () ->
         @sample_vals = (sample.value for sample in @sample_list when sample.value != null)
 
-        @attributes = (key for key of @sample_list[0]["extra_attributes"])
-        console.log("attributes:", @attributes)
-        @sample_attr_vals = []
-        if @attributes.length > 0
-            for sample in @sample_list
-                attr_vals = {}
-                for attribute in @attributes
-                    attr_vals[attribute] = sample["extra_attributes"][attribute]
-                @sample_attr_vals.push(attr_vals)
-        @samples = _.zip(@sample_names, @sample_vals, @sample_attr_vals)
-
     create_svg: () ->
         svg = d3.select("#histogram")
           .append("svg")
@@ -51,18 +36,19 @@ class Histogram
             .attr("height", @plot_height + @margin.top + @margin.bottom)
           .append("g")
             .attr("transform", "translate(" + @margin.left + "," + @margin.top + ")")
-            
+
         return svg
-        
+
     create_x_scale: () ->
+        console.log("min/max:", d3.min(@sample_vals) + "," + d3.max(@sample_vals))
         @x_scale = d3.scale.linear()
             .domain([d3.min(@sample_vals), d3.max(@sample_vals)])
-            .range([0, @plot_width])    
+            .range([0, @plot_width]) 
 
     get_histogram_data: () ->
         console.log("sample_vals:", @sample_vals)
         @histogram_data = d3.layout.histogram()
-            .bins(@x_scale.ticks(10))(@sample_vals)
+            .bins(@x_scale.ticks(20))(@sample_vals)
         console.log("histogram_data:", @histogram_data[0])
 
     create_y_scale: () ->
@@ -71,12 +57,9 @@ class Histogram
             .range([@plot_height, 0])
 
     create_graph: () ->
-        
         @add_x_axis()
-        #@add_y_axis() 
-
         @add_bars()
-        
+
     add_x_axis: () ->
         x_axis = d3.svg.axis()
             .scale(@x_scale)
@@ -86,64 +69,37 @@ class Histogram
             .attr("class", "x axis")
             .attr("transform", "translate(0," + @plot_height + ")")
             .call(x_axis)
-            #.selectAll("text")  
-            #    .style("text-anchor", "end")
-            #    .style("font-size", "12px")
-            #    .attr("dx", "-.8em")
-            #    .attr("dy", "-.3em")
-            #    .attr("transform", (d) =>
-            #        return "rotate(-90)" 
-            #    )
-
-    #add_y_axis: () ->
-    #    y_axis = d3.svg.axis()
-    #            .scale(@y_scale)
-    #            .orient("left")
-    #            .ticks(5)
-    #
-    #    @svg.append("g")
-    #        .attr("class", "y axis")
-    #        .call(y_axis)
-    #      .append("text")
-    #        .attr("transform", "rotate(-90)")
-    #        .attr("y", 6)
-    #        .attr("dy", ".71em")
-    #        .style("text-anchor", "end")
-
+            
+    add_y_axis: () ->
+        y_axis = d3.svg.axis()
+                .scale(@y_scale)
+                .orient("left")
+                .ticks(5)
     add_bars: () ->
-        @svg.selectAll(".bar")
+        console.log("bar_width:", @x_scale(@histogram_data[0].dx))
+        bar = @svg.selectAll(".bar")
             .data(@histogram_data)
           .enter().append("g")
             .attr("class", "bar")
             .attr("transform", (d) =>
-                return "translate(" + @margin.left + "," + @margin.top + ")")
-          .append("rect")
+                return "translate(" + @x_scale(d.x) + "," + @y_scale(d.y) + ")")
+        
+        bar.append("rect")
             .attr("x", 1)
-            .attr("width", @x_scale(@histogram_data[0].dx) - 1)
+            .attr("width", (@x_scale(@histogram_data[1].x) - @x_scale(@histogram_data[0].x)) - 1)
             .attr("height", (d) =>
                 return @plot_height - @y_scale(d.y)
             )
-          .append("text")
+        bar.append("text")
             .attr("dy", ".75em")
             .attr("y", 6)
-            .attr("x", @x_scale(@histogram_data[0].dx) / 2)
+            .attr("x", (@x_scale(@histogram_data[1].x) - @x_scale(@histogram_data[0].x))/2)
             .attr("text-anchor", "middle")
+            .style("fill", "#fff")
             .text((d) =>
-                return @format_count(d.y)
+                bar_height = @plot_height - @y_scale(d.y)
+                if bar_height > 20
+                    return @format_count(d.y)
             )
 
-    #open_trait_selection: () ->
-    #    $('#collections_holder').load('/collections/list?color_by_trait #collections_list', =>
-    #        $.colorbox(
-    #            inline: true
-    #            href: "#collections_holder"
-    #        )
-    #        #Removes the links from the collection names, because clicking them would leave the page
-    #        #instead of loading the list of traits in the colorbox
-    #        $('a.collection_name').attr( 'onClick', 'return false' )
-    #        #$('.collection_name').each (index, element) =>
-    #        #    console.log("contents:", $(element).contents())
-    #        #    $(element).contents().unwrap()
-    #    )
-
 root.Histogram = Histogram
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/histogram.js b/wqflask/wqflask/static/new/javascript/histogram.js
index e7926ab1..eb00ca73 100644
--- a/wqflask/wqflask/static/new/javascript/histogram.js
+++ b/wqflask/wqflask/static/new/javascript/histogram.js
@@ -11,7 +11,7 @@
       this.sample_group = sample_group;
       this.sort_by = "name";
       this.format_count = d3.format(",.0f");
-      this.get_samples();
+      this.get_sample_vals();
       this.margin = {
         top: 10,
         right: 30,
@@ -32,21 +32,9 @@
       this.create_graph();
     }
 
-    Histogram.prototype.get_samples = function() {
-      var attr_vals, attribute, key, sample, _i, _j, _len, _len1, _ref, _ref1;
-      this.sample_names = (function() {
-        var _i, _len, _ref, _results;
-        _ref = this.sample_list;
-        _results = [];
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          if (sample.value !== null) {
-            _results.push(sample.name);
-          }
-        }
-        return _results;
-      }).call(this);
-      this.sample_vals = (function() {
+    Histogram.prototype.get_sample_vals = function() {
+      var sample;
+      return this.sample_vals = (function() {
         var _i, _len, _ref, _results;
         _ref = this.sample_list;
         _results = [];
@@ -58,30 +46,6 @@
         }
         return _results;
       }).call(this);
-      this.attributes = (function() {
-        var _results;
-        _results = [];
-        for (key in this.sample_list[0]["extra_attributes"]) {
-          _results.push(key);
-        }
-        return _results;
-      }).call(this);
-      console.log("attributes:", this.attributes);
-      this.sample_attr_vals = [];
-      if (this.attributes.length > 0) {
-        _ref = this.sample_list;
-        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-          sample = _ref[_i];
-          attr_vals = {};
-          _ref1 = this.attributes;
-          for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
-            attribute = _ref1[_j];
-            attr_vals[attribute] = sample["extra_attributes"][attribute];
-          }
-          this.sample_attr_vals.push(attr_vals);
-        }
-      }
-      return this.samples = _.zip(this.sample_names, this.sample_vals, this.sample_attr_vals);
     };
 
     Histogram.prototype.create_svg = function() {
@@ -91,12 +55,13 @@
     };
 
     Histogram.prototype.create_x_scale = function() {
+      console.log("min/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]);
     };
 
     Histogram.prototype.get_histogram_data = function() {
       console.log("sample_vals:", this.sample_vals);
-      this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(10))(this.sample_vals);
+      this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(20))(this.sample_vals);
       return console.log("histogram_data:", this.histogram_data[0]);
     };
 
@@ -120,14 +85,27 @@
       return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis);
     };
 
+    Histogram.prototype.add_y_axis = function() {
+      var y_axis;
+      return y_axis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5);
+    };
+
     Histogram.prototype.add_bars = function() {
-      var _this = this;
-      return this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", function(d) {
-        return "translate(" + _this.margin.left + "," + _this.margin.top + ")";
-      }).append("rect").attr("x", 1).attr("width", this.x_scale(this.histogram_data[0].dx) - 1).attr("height", function(d) {
+      var bar,
+        _this = this;
+      console.log("bar_width:", this.x_scale(this.histogram_data[0].dx));
+      bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", function(d) {
+        return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")";
+      });
+      bar.append("rect").attr("x", 1).attr("width", (this.x_scale(this.histogram_data[1].x) - this.x_scale(this.histogram_data[0].x)) - 1).attr("height", function(d) {
         return _this.plot_height - _this.y_scale(d.y);
-      }).append("text").attr("dy", ".75em").attr("y", 6).attr("x", this.x_scale(this.histogram_data[0].dx) / 2).attr("text-anchor", "middle").text(function(d) {
-        return _this.format_count(d.y);
+      });
+      return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", (this.x_scale(this.histogram_data[1].x) - this.x_scale(this.histogram_data[0].x)) / 2).attr("text-anchor", "middle").style("fill", "#fff").text(function(d) {
+        var bar_height;
+        bar_height = _this.plot_height - _this.y_scale(d.y);
+        if (bar_height > 20) {
+          return _this.format_count(d.y);
+        }
       });
     };
 
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index f5f13c27..93d3b5de 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()
@@ -30,7 +30,10 @@ $ ->
             @y_max = d3.max(@y_coords) * 1.2
 
             @svg = @create_svg()
+            console.log("svg created")
             @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names)
+            #console.log("coordinates:", @plot_coordinates)
+            
             
             @plot_height -= @y_buffer
             @create_scales()
@@ -73,6 +76,7 @@ $ ->
         create_coordinates: () -> 
             chr_lengths = []
             chr_seen = []
+            #console.log("total_length2:", @total_length)
             for result in js_data.qtl_results
                 if result.chr == "X"
                     chr_length = parseFloat(@chromosomes[20])
@@ -80,12 +84,16 @@ $ ->
                     chr_length = parseFloat(@chromosomes[result.chr])
                 if not(result.chr in chr_seen)
                     chr_seen.push(result.chr) 
-                    chr_lengths.push(chr_length) 
-                    if result.chr != "1"
+                    chr_lengths.push(chr_length)
+                    #console.log("result.chr:", result.chr)
+                    if result.chr != 1
                         @total_length += parseFloat(chr_lengths[chr_lengths.length - 2])
-                @x_coords.push(@total_length + parseFloat(result.Mb))
-                @y_coords.push(result.lod_score)
-                @marker_names.push(result.name)
+                #console.log("total_length3:", @total_length)
+                #console.log("Mb:", result.Mb)
+                if result.lod_score > 2
+                    @x_coords.push(@total_length + parseFloat(result.Mb))
+                    @y_coords.push(result.lod_score)
+                    @marker_names.push(result.name)
             @total_length += parseFloat(chr_lengths[chr_lengths.length-1])
             #console.log("chr_lengths: ", chr_lengths)
 
@@ -141,12 +149,19 @@ $ ->
                 .style("stroke", "#000")
 
         create_scales: () ->
+            #@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, d3.max(@x_coords)])
+                .domain([0, (@total_length + @chromosomes['24'])])
                 .range([@x_buffer, @plot_width])
 
             @y_scale = d3.scale.linear()
-                .domain([0, @y_max])
+                .domain([2, @y_max])
                 .range([@plot_height, @y_buffer])
 
         create_x_axis_tick_values: () ->
@@ -230,13 +245,13 @@ $ ->
                 .style("stroke", "#ccc")
                 
         fill_chr_areas: () ->
-            @svg.selectAll("rect.chr_fill_area_1")
+            @svg.selectAll("rect.chr_fill_area")
                 .data(_.zip(@chr_lengths, @cumulative_chr_lengths), (d) =>
                     return d
                 )
                 .enter()
                 .append("rect")
-                .attr("class", "chr_fill_area_1")
+                .attr("class", "chr_fill_area")
                 .attr("x", (d, i) =>
                     if i == 0
                         return @x_scale(0)
@@ -247,7 +262,8 @@ $ ->
                 .attr("width", (d) =>
                     return @x_scale(d[0])
                 )
-                .attr("height", @plot_height-@y_buffer)                
+                .attr("height", @plot_height-@y_buffer)
+                .attr("fill", "none")
 
         add_chr_labels: () ->
             chr_names = []
@@ -279,10 +295,10 @@ $ ->
                 .enter()
                 .append("circle")
                 .attr("cx", (d) =>
-                    return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * d[0]/parseFloat(@x_max))
+                    return @x_scale(d[0])
                 )
                 .attr("cy", (d) =>
-                    return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
+                    return @y_scale(d[1])
                 )
                 .attr("r", 2)
                 .attr("id", (d) =>
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index cdf37671..8e5b6c11 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -20,7 +20,6 @@
         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];
@@ -31,6 +30,7 @@
         console.log("@x_buffer: ", this.x_buffer);
         this.y_max = d3.max(this.y_coords) * 1.2;
         this.svg = this.create_svg();
+        console.log("svg created");
         this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
         this.plot_height -= this.y_buffer;
         this.create_scales();
@@ -93,13 +93,15 @@
           if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
             chr_seen.push(result.chr);
             chr_lengths.push(chr_length);
-            if (result.chr !== "1") {
+            if (result.chr !== 1) {
               this.total_length += parseFloat(chr_lengths[chr_lengths.length - 2]);
             }
           }
-          this.x_coords.push(this.total_length + parseFloat(result.Mb));
-          this.y_coords.push(result.lod_score);
-          this.marker_names.push(result.name);
+          if (result.lod_score > 2) {
+            this.x_coords.push(this.total_length + parseFloat(result.Mb));
+            this.y_coords.push(result.lod_score);
+            this.marker_names.push(result.name);
+          }
         }
         return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
       };
@@ -150,8 +152,12 @@
       };
 
       Manhattan_Plot.prototype.create_scales = function() {
-        this.x_scale = d3.scale.linear().domain([0, d3.max(this.x_coords)]).range([this.x_buffer, this.plot_width]);
-        return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
+        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]);
+        return this.y_scale = d3.scale.linear().domain([2, this.y_max]).range([this.plot_height, this.y_buffer]);
       };
 
       Manhattan_Plot.prototype.create_x_axis_tick_values = function() {
@@ -224,9 +230,9 @@
 
       Manhattan_Plot.prototype.fill_chr_areas = function() {
         var _this = this;
-        return this.svg.selectAll("rect.chr_fill_area_1").data(_.zip(this.chr_lengths, this.cumulative_chr_lengths), function(d) {
+        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_1").attr("x", function(d, i) {
+        }).enter().append("rect").attr("class", "chr_fill_area").attr("x", function(d, i) {
           if (i === 0) {
             return _this.x_scale(0);
           } else {
@@ -234,7 +240,7 @@
           }
         }).attr("y", this.y_buffer).attr("width", function(d) {
           return _this.x_scale(d[0]);
-        }).attr("height", this.plot_height - this.y_buffer);
+        }).attr("height", this.plot_height - this.y_buffer).attr("fill", "none");
       };
 
       Manhattan_Plot.prototype.add_chr_labels = function() {
@@ -257,9 +263,9 @@
       Manhattan_Plot.prototype.add_plot_points = function() {
         var _this = this;
         return this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
-          return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
+          return _this.x_scale(d[0]);
         }).attr("cy", function(d) {
-          return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
+          return _this.y_scale(d[1]);
         }).attr("r", 2).attr("id", function(d) {
           return "point_" + String(d[2]);
         }).classed("circle", true).on("mouseover", function(d) {
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.coffee b/wqflask/wqflask/static/new/javascript/show_trait.coffee
index e42a7d82..e45bb0be 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.coffee
+++ b/wqflask/wqflask/static/new/javascript/show_trait.coffee
@@ -64,7 +64,8 @@ $ ->
     sample_lists = js_data.sample_lists
     sample_group_types = js_data.sample_group_types
 
-    $("#update_bar_chart.btn-group").button()
+    #if $("#update_bar_chart").length
+    #    $("#update_bar_chart.btn-group").button()
     root.bar_chart = new Bar_Chart(sample_lists[0])
     root.histogram = new Histogram(sample_lists[0])
     new Box_Plot(sample_lists[0])
diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js
index d3a34166..c28b05f5 100644
--- a/wqflask/wqflask/static/new/javascript/show_trait.js
+++ b/wqflask/wqflask/static/new/javascript/show_trait.js
@@ -61,7 +61,6 @@
     var block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, populate_sample_attributes_values_dropdown, process_id, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values;
     sample_lists = js_data.sample_lists;
     sample_group_types = js_data.sample_group_types;
-    $("#update_bar_chart.btn-group").button();
     root.bar_chart = new Bar_Chart(sample_lists[0]);
     root.histogram = new Histogram(sample_lists[0]);
     new Box_Plot(sample_lists[0]);
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 64d2e9b7..c1d4d7e5 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -26,6 +26,7 @@
                 Genome Association Results
             </h2>
         </div>
+
         <table cellpadding="0" cellspacing="0" border="0" id="qtl_results" class="table table-hover table-striped table-bordered">
             <thead>
                 <tr>
@@ -61,7 +62,7 @@
     </script>
 
     <!--[if lt IE 9]>
-        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>
+<!--        <script language="javascript" type="text/javascript" src="/static/packages/jqplot/excanvas.js"></script>-->
     <![endif]-->
     <script language="javascript" type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait.html b/wqflask/wqflask/templates/show_trait.html
index 26f21f08..8822fd00 100644
--- a/wqflask/wqflask/templates/show_trait.html
+++ b/wqflask/wqflask/templates/show_trait.html
@@ -64,4 +64,45 @@
     <script type="text/javascript" src="/static/new/javascript/show_trait_mapping_tools.js"></script>
     <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>
+    
+    <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_edit_data.html b/wqflask/wqflask/templates/show_trait_edit_data.html
index 84c606b9..e7df3b13 100644
--- a/wqflask/wqflask/templates/show_trait_edit_data.html
+++ b/wqflask/wqflask/templates/show_trait_edit_data.html
@@ -82,75 +82,73 @@
         <div>
             <h3>{{ sample_type.header }}</h3>
 
-            <table class="table table-hover table-striped"  {# Todo: Enable sorting on table #}
+            <table cellpadding="0" cellspacing="0" border="0" class="table table-hover table-striped table-bordered"
                    id="samples_{{ sample_type.sample_group_type }}">
-                <tr>
-                    <th>Index</th>
-
-                    <th>Sample</th>
-
-                    <th>Value</th>
-                    {% if sample_type.se_exists() %}
-                    <th>&nbsp;</th>
-
-                    <th>SE</th>
-                    {% endif %}
-
-                    {% for attribute in sample_type.attributes|sort() %}
-                    <th>
-                        {{ sample_type.attributes[attribute].name }}
-                    </th>
+                <thead>
+                    <tr>
+                        <td>Index</td>
+                        <td>Sample</td>
+                        <td>Value</td>
+                        {% if sample_type.se_exists() %}
+                        <td>&nbsp;</td>
+                        <td>SE</td>
+                        {% endif %}
+                        {% for attribute in sample_type.attributes|sort() %}
+                        <td>
+                            {{ sample_type.attributes[attribute].name }}
+                        </td>
+                        {% endfor %}
+                    </tr>
+                </thead>
+                <tbody>
+                    {% for sample in sample_type.sample_list %}
+                    <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}">
+                        <td class="column_name-Index">
+                            {{ loop.index }}
+                            <input type="checkbox" name="selectCheck"
+                                   class="checkbox edit_sample_checkbox"
+                                   value="{{ sample.name }}" checked="checked">
+                        </td>
+        
+                        <td class="column_name-Sample">
+                            <span class="edit_sample_sample_name">
+                                {{ sample.name }}
+                             </span>
+                        </td>
+        
+                        {# Todo: Add IDs #}
+                        <td class="column_name-Value">
+                          <input type="text" data-value="{{ sample.display_value }}" name="{{ 'value:' + sample.name }}"
+                                 class="trait_value_input edit_sample_value"
+                                 value="{{ sample.display_value }}"
+                                 size=8 maxlength=8
+                          >
+                        </td>
+        
+                        {% if sample_type.se_exists() %}
+                        <td>
+                          ±
+                        </td>
+        
+                        {# Todo: Add IDs #}
+                        <td class="column_name-SE">
+                          <input type="text" data-value="{{ sample.display_variance }}" name="{{ 'variance:' + sample.name}}"
+                                 class="trait_value_input edit_sample_se"
+                                 value="{{ sample.display_variance }}"
+                                 size=8 maxlength=8
+                          >
+                        </td>
+                        {% endif %}
+        
+                        {# Loop through each attribute type and input value #}
+                        {% for attribute in sample_type.attributes|sort() %}
+                        <td class="std_cell column_name-{{ sample_type.attributes[attribute].name.replace(' ', '_') }}">
+                          {{ sample.extra_attributes[sample_type.attributes[attribute].name] }}
+                        </td>
+                        {% endfor %}
+                    </tr>
                     {% endfor %}
-                </tr>
-
-                {% for sample in sample_type.sample_list %}
-                <tr class="{{ sample.class_outlier }} value_se" id="{{ sample.this_id }}">
-                <td class="column_name-Index">
-                    {{ loop.index }}
-                    <input type="checkbox" name="selectCheck"
-                           class="checkbox edit_sample_checkbox"
-                           value="{{ sample.name }}" checked="checked">
-                </td>
-
-                <td class="column_name-Sample">
-                    <span class="edit_sample_sample_name">
-                        {{ sample.name }}
-                     </span>
-                </td>
-
-                {# Todo: Add IDs #}
-                <td class="column_name-Value">
-                  <input type="text" data-value="{{ sample.display_value }}" name="{{ 'value:' + sample.name }}"
-                         class="trait_value_input edit_sample_value"
-                         value="{{ sample.display_value }}"
-                         size=8 maxlength=8
-                  >
-                </td>
-
-                {% if sample_type.se_exists() %}
-                <td>
-                  ±
-                </td>
-
-                {# Todo: Add IDs #}
-                <td class="column_name-SE">
-                  <input type="text" data-value="{{ sample.display_variance }}" name="{{ 'variance:' + sample.name}}"
-                         class="trait_value_input edit_sample_se"
-                         value="{{ sample.display_variance }}"
-                         size=8 maxlength=8
-                  >
-                </td>
-                {% endif %}
-
-                {# Loop through each attribute type and input value #}
-                {% for attribute in sample_type.attributes|sort() %}
-                <td class="std_cell column_name-{{ sample_type.attributes[attribute].name.replace(' ', '_') }}">
-                  {{ sample.extra_attributes[sample_type.attributes[attribute].name] }}
-                </td>
-                {% endfor %}
-              </tr>
-              {% endfor %}
-
+                </tbody>
             </table>
         </div>
         {% endfor %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 828199c5..89820145 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -243,7 +243,12 @@ def marker_regression_page():
             print("  ---**--- {}: {}".format(type(template_vars.__dict__[item]), item))
 
         #causeerror
-        Redis.set(key, pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
+        
+        #qtl_length = len(result['js_data']['qtl_results'])
+        #print("qtl_length:", qtl_length)
+        pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+        print("pickled result length:", len(pickled_result))
+        Redis.set(key, pickled_result)
         Redis.expire(key, 60*60)
 
     with Bench("Rendering template"):
-- 
cgit v1.2.3