2 files changed, 23 insertions, 12 deletions

diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 4c67c5a5..2b09fbc8 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -5,29 +5,31 @@ $ ->
             @chromosomes = js_data.chromosomes
 
             @total_length = 0
-            
+
             @max_chr = @get_max_chr()
-            @scaled_chr_lengths = @get_chr_lengths()
 
             @x_coords = []
             @y_coords = []
             @marker_names = []    
             @create_coordinates()
+            @scaled_chr_lengths = @get_chr_lengths()
 
             # Buffer to allow for the ticks/labels to be drawn
-            @x_buffer = @plot_width/30
+            @x_buffer = @plot_width/25
             @y_buffer = @plot_height/20
             
-            @x_max = d3.max(@x_coords)
+            #@x_max = d3.max(@x_coords)
+            console.log("x_max is", d3.max(@x_coords))
+            @x_max = @total_length
+            console.log("x_max is", @x_max)
             @y_max = d3.max(@y_coords) * 1.2
 
             @svg = @create_svg()
             @plot_coordinates = _.zip(@x_coords, @y_coords, @marker_names)
-            @plot_height = @plot_height - @y_buffer
+            @plot_height -= @y_buffer
             @create_scales()
             @create_graph()
 
-
         get_max_chr: () ->
             max_chr = 0
             for result in @qtl_results
@@ -52,6 +54,8 @@ $ ->
                 this_length = @chromosomes[key]
                 cumulative_chr_lengths.push(total_length + this_length)
                 total_length += this_length
+                
+            console.log("total length is:", total_length)
 
             return cumulative_chr_lengths
 
@@ -69,6 +73,8 @@ $ ->
                 @x_coords.push(@total_length + parseFloat(result.Mb))
                 @y_coords.push(result.lod_score)
                 @marker_names.push(result.name)
+            @total_length += chr_lengths[chr_lengths.length-1]
+            console.log("total length is", @total_length)
 
             console.log("chr_lengths are:", chr_lengths)
 
@@ -93,7 +99,7 @@ $ ->
 
         create_scales: () ->
             @x_scale = d3.scale.linear()
-                .domain([0, @x_max])
+                .domain([0, d3.max(@x_coords)])
                 .range([@x_buffer, @plot_width])
 
             @y_scale = d3.scale.linear()
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index 8b99b28f..38d88208 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -13,18 +13,20 @@
         this.chromosomes = js_data.chromosomes;
         this.total_length = 0;
         this.max_chr = this.get_max_chr();
-        this.scaled_chr_lengths = this.get_chr_lengths();
         this.x_coords = [];
         this.y_coords = [];
         this.marker_names = [];
         this.create_coordinates();
-        this.x_buffer = this.plot_width / 30;
+        this.scaled_chr_lengths = this.get_chr_lengths();
+        this.x_buffer = this.plot_width / 25;
         this.y_buffer = this.plot_height / 20;
-        this.x_max = d3.max(this.x_coords);
+        console.log("x_max is", d3.max(this.x_coords));
+        this.x_max = this.total_length;
+        console.log("x_max is", this.x_max);
         this.y_max = d3.max(this.y_coords) * 1.2;
         this.svg = this.create_svg();
         this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names);
-        this.plot_height = this.plot_height - this.y_buffer;
+        this.plot_height -= this.y_buffer;
         this.create_scales();
         this.create_graph();
       }
@@ -61,6 +63,7 @@
           cumulative_chr_lengths.push(total_length + this_length);
           total_length += this_length;
         }
+        console.log("total length is:", total_length);
         return cumulative_chr_lengths;
       };
 
@@ -84,6 +87,8 @@
           this.y_coords.push(result.lod_score);
           this.marker_names.push(result.name);
         }
+        this.total_length += chr_lengths[chr_lengths.length - 1];
+        console.log("total length is", this.total_length);
         return console.log("chr_lengths are:", chr_lengths);
       };
 
@@ -107,7 +112,7 @@
       };
 
       Manhattan_Plot.prototype.create_scales = function() {
-        this.x_scale = d3.scale.linear().domain([0, this.x_max]).range([this.x_buffer, this.plot_width]);
+        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]);
       };