Fixed issue where points in marker regression manhattan plot

weren't positioned on the x-axis

2 files changed, 26 insertions, 10 deletions

diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 2221e030..2892987e 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -25,6 +25,8 @@ $ ->
             
             #@x_max = d3.max(@x_coords)
             @x_max = @total_length
+            console.log("@x_max: ", @x_max)
+            console.log("@x_buffer: ", @x_buffer)
             @y_max = d3.max(@y_coords) * 1.2
 
             @svg = @create_svg()
@@ -53,6 +55,8 @@ $ ->
             
             ###
             
+            console.log("@chromosomes: ", @chromosomes)
+            
             cumulative_chr_lengths = []
             chr_lengths = []
             total_length = 0
@@ -61,8 +65,8 @@ $ ->
                 chr_lengths.push(this_length)
                 cumulative_chr_lengths.push(total_length + this_length)
                 total_length += this_length
-                
-            #console.log("total length is:", total_length)
+
+            console.log("chr_lengths: ", chr_lengths)
 
             return [chr_lengths, cumulative_chr_lengths]
 
@@ -70,16 +74,20 @@ $ ->
             chr_lengths = []
             chr_seen = []
             for result in js_data.qtl_results
-                chr_length = @chromosomes[result.chr]
+                if result.chr == "X"
+                    chr_length = parseFloat(@chromosomes[20])
+                else
+                    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"
-                        @total_length += chr_lengths[chr_lengths.length - 2]
+                        @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)
-            @total_length += chr_lengths[chr_lengths.length-1]
+            @total_length += parseFloat(chr_lengths[chr_lengths.length-1])
+            #console.log("chr_lengths: ", chr_lengths)
 
         show_marker_in_table: (marker_info) ->
             console.log("in show_marker_in_table")
@@ -271,7 +279,7 @@ $ ->
                 .enter()
                 .append("circle")
                 .attr("cx", (d) =>
-                    return parseFloat(@x_buffer + ((@plot_width-@x_buffer) * d[0]/@x_max))
+                    return parseFloat(@x_buffer) + ((parseFloat(@plot_width)-parseFloat(@x_buffer)) * d[0]/parseFloat(@x_max))
                 )
                 .attr("cy", (d) =>
                     return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index a2b2ff57..ffcf1a75 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -27,6 +27,8 @@
         this.x_buffer = this.plot_width / 30;
         this.y_buffer = this.plot_height / 20;
         this.x_max = this.total_length;
+        console.log("@x_max: ", this.x_max);
+        console.log("@x_buffer: ", this.x_buffer);
         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);
@@ -61,6 +63,7 @@
         */
 
         var chr_lengths, cumulative_chr_lengths, key, this_length, total_length;
+        console.log("@chromosomes: ", this.chromosomes);
         cumulative_chr_lengths = [];
         chr_lengths = [];
         total_length = 0;
@@ -70,6 +73,7 @@
           cumulative_chr_lengths.push(total_length + this_length);
           total_length += this_length;
         }
+        console.log("chr_lengths: ", chr_lengths);
         return [chr_lengths, cumulative_chr_lengths];
       };
 
@@ -80,19 +84,23 @@
         _ref = js_data.qtl_results;
         for (_i = 0, _len = _ref.length; _i < _len; _i++) {
           result = _ref[_i];
-          chr_length = this.chromosomes[result.chr];
+          if (result.chr === "X") {
+            chr_length = parseFloat(this.chromosomes[20]);
+          } else {
+            chr_length = parseFloat(this.chromosomes[result.chr]);
+          }
           if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
             chr_seen.push(result.chr);
             chr_lengths.push(chr_length);
             if (result.chr !== "1") {
-              this.total_length += chr_lengths[chr_lengths.length - 2];
+              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);
         }
-        return this.total_length += chr_lengths[chr_lengths.length - 1];
+        return this.total_length += parseFloat(chr_lengths[chr_lengths.length - 1]);
       };
 
       Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) {
@@ -248,7 +256,7 @@
       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 + ((_this.plot_width - _this.x_buffer) * d[0] / _this.x_max));
+          return parseFloat(_this.x_buffer) + ((parseFloat(_this.plot_width) - parseFloat(_this.x_buffer)) * d[0] / parseFloat(_this.x_max));
         }).attr("cy", function(d) {
           return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
         }).attr("r", 2).attr("id", function(d) {