Fixed the issue with the x-axis coordinates for marker regression plot

3 files changed, 16 insertions, 19 deletions

diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index a6134fdd..2e8f020d 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -93,6 +93,7 @@ def run_human(pheno_vector,
         result_store = []
         identifier = uuid.uuid4()
         for part, result in enumerate(results):
+            # todo: Don't use TempData here. Instead revert old one and store this stuff as a list
             data_store = temp_data.TempData(identifier, "plink", part)
             
             data_store.store("data", pickle.dumps(result, pickle.HIGHEST_PROTOCOL))
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index fd1fac54..2f8da6dc 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -4,18 +4,17 @@ $ ->
             @qtl_results = js_data.qtl_results
             console.log("qtl_results are:", @qtl_results)
             @chromosomes = js_data.chromosomes
-            console.log("chromosomes: ", @chromosomes)
 
             @total_length = 0
 
             @max_chr = @get_max_chr()
-            console.log("max_chr is: ", @max_chr)
 
             @x_coords = []
             @y_coords = []
             @marker_names = []
             console.time('Create coordinates')
             @create_coordinates()
+            console.log("@x_coords: ", @x_coords)
             console.timeEnd('Create coordinates')
             [@chr_lengths, @cumulative_chr_lengths] = @get_chr_lengths()
 
@@ -25,7 +24,6 @@ $ ->
             
             #@x_max = d3.max(@x_coords)
             @x_max = @total_length
-            @y_min = d3.min(@y_coords)
             @y_max = d3.max(@y_coords) * 1.2
 
             @svg = @create_svg()
@@ -58,7 +56,7 @@ $ ->
             chr_lengths = []
             total_length = 0
             for key of @chromosomes
-                this_length = @chromosomes[key][1]
+                this_length = @chromosomes[key]
                 chr_lengths.push(this_length)
                 cumulative_chr_lengths.push(total_length + this_length)
                 total_length += this_length
@@ -71,11 +69,10 @@ $ ->
             chr_lengths = []
             chr_seen = []
             for result in js_data.qtl_results
-                chr_length = @chromosomes[result.chr][1]
+                chr_length = @chromosomes[result.chr]
                 if not(result.chr in chr_seen)
                     chr_seen.push(result.chr) 
-                    chr_lengths.push(chr_length)
-                        
+                    chr_lengths.push(chr_length) 
                     if result.chr != "1"
                         @total_length += chr_lengths[chr_lengths.length - 2]
                 @x_coords.push(@total_length + parseFloat(result.Mb))
@@ -106,7 +103,7 @@ $ ->
             @add_x_axis()
             @add_y_axis()
             @add_chr_lines()
-            #@fill_chr_areas()
+            @fill_chr_areas()
             @add_chr_labels()
             @add_plot_points()
 
@@ -140,7 +137,7 @@ $ ->
                 .range([@x_buffer, @plot_width])
 
             @y_scale = d3.scale.linear()
-                .domain([@y_min, @y_max])
+                .domain([0, @y_max])
                 .range([@plot_height, @y_buffer])
 
         create_x_axis_tick_values: () ->
@@ -246,7 +243,7 @@ $ ->
         add_chr_labels: () ->
             chr_names = []
             for key of @chromosomes
-                chr_names.push(@chromosomes[key][0])
+                chr_names.push(key)
             chr_info = _.zip(chr_names, @chr_lengths, @cumulative_chr_lengths)
             @svg.selectAll("text")
                 .data(chr_info, (d) =>
@@ -276,7 +273,7 @@ $ ->
                     return @x_buffer + ((@plot_width-@x_buffer) * d[0]/@x_max)
                 )
                 .attr("cy", (d) =>
-                    return @plot_height - ((@plot_height-@y_buffer) * (d[1]-@y_min)/@y_max)
+                    return @plot_height - ((@plot_height-@y_buffer) * d[1]/@y_max)
                 )
                 .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 37a4e1e5..50578125 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -13,21 +13,19 @@
         this.qtl_results = js_data.qtl_results;
         console.log("qtl_results are:", this.qtl_results);
         this.chromosomes = js_data.chromosomes;
-        console.log("chromosomes: ", this.chromosomes);
         this.total_length = 0;
         this.max_chr = this.get_max_chr();
-        console.log("max_chr is: ", this.max_chr);
         this.x_coords = [];
         this.y_coords = [];
         this.marker_names = [];
         console.time('Create coordinates');
         this.create_coordinates();
+        console.log("@x_coords: ", this.x_coords);
         console.timeEnd('Create coordinates');
         _ref = this.get_chr_lengths(), this.chr_lengths = _ref[0], this.cumulative_chr_lengths = _ref[1];
         this.x_buffer = this.plot_width / 30;
         this.y_buffer = this.plot_height / 20;
         this.x_max = this.total_length;
-        this.y_min = d3.min(this.y_coords);
         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);
@@ -66,7 +64,7 @@
         chr_lengths = [];
         total_length = 0;
         for (key in this.chromosomes) {
-          this_length = this.chromosomes[key][1];
+          this_length = this.chromosomes[key];
           chr_lengths.push(this_length);
           cumulative_chr_lengths.push(total_length + this_length);
           total_length += this_length;
@@ -81,7 +79,7 @@
         _ref = js_data.qtl_results;
         for (_i = 0, _len = _ref.length; _i < _len; _i++) {
           result = _ref[_i];
-          chr_length = this.chromosomes[result.chr][1];
+          chr_length = this.chromosomes[result.chr];
           if (!(_ref1 = result.chr, __indexOf.call(chr_seen, _ref1) >= 0)) {
             chr_seen.push(result.chr);
             chr_lengths.push(chr_length);
@@ -121,6 +119,7 @@
         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();
       };
@@ -142,7 +141,7 @@
 
       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([this.y_min, this.y_max]).range([this.plot_height, this.y_buffer]);
+        return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]);
       };
 
       Manhattan_Plot.prototype.create_x_axis_tick_values = function() {
@@ -233,7 +232,7 @@
           _this = this;
         chr_names = [];
         for (key in this.chromosomes) {
-          chr_names.push(this.chromosomes[key][0]);
+          chr_names.push(key);
         }
         chr_info = _.zip(chr_names, this.chr_lengths, this.cumulative_chr_lengths);
         return this.svg.selectAll("text").data(chr_info, function(d) {
@@ -250,7 +249,7 @@
         return this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
           return _this.x_buffer + ((_this.plot_width - _this.x_buffer) * d[0] / _this.x_max);
         }).attr("cy", function(d) {
-          return _this.plot_height - ((_this.plot_height - _this.y_buffer) * (d[1] - _this.y_min) / _this.y_max);
+          return _this.plot_height - ((_this.plot_height - _this.y_buffer) * d[1] / _this.y_max);
         }).attr("r", 2).attr("id", function(d) {
           return "point_" + String(d[2]);
         }).classed("circle", true).on("mouseover", function(d) {