Put coffeescript code for manhattan plot into a class/functions

2 files changed, 124 insertions, 93 deletions

diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 6a10d95e..4ea35593 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -1,56 +1,63 @@
 $ ->
 
-    x_coords = []
-    y_coords = []
-    
-    largest_chr = 0
-    for result in js_data.qtl_results
-        chr = parseInt(result.chr)
-        console.log("foo:", chr, typeof(chr))
-        if _.isNaN(chr) 
-            console.log("Got NaN")
-        else
-            if chr > largest_chr
-                largest_chr = chr
-                
-    console.log("largest_chr is:", largest_chr)
-    
-    for result in js_data.qtl_results
-        chr = parseInt(result.chr)
-        if _.isNaN(chr)
-            if result.chr == "X"
-                chr = largest_chr + 1
-            else if result.chr == "Y"
-                chr = largest_chr + 2
-
-        x_coords.push((chr * 200) + parseFloat(result.Mb))
-        y_coords.push(result.lrs_value)
-        #plot_coordinates.push([x_coord, y_coord])
-
-    x_max = d3.max(x_coords)
-    y_max = d3.max(y_coords)
-        
-    plot_coordinates = _.zip(x_coords, y_coords)
+    class Manhattan_Plot
+
+        constructor: ->
+            @qtl_results = js_data.qtl_results
+            @max_chr = @get_max_chr()
+            
+            @x_coords = []
+            @y_coords = []
+            @get_coordinates()
+            
+            @x_max = d3.max(@x_coords)
+            @y_max = d3.max(@y_coords)
+            
+            @plot_coordinates = _.zip(@x_coords, @y_coords)
+            @create_graph()
+
+
+        get_max_chr: () ->
+            max_chr = 0
+            for result in @qtl_results
+                chr = parseInt(result.chr)
+                console.log("foo:", chr, typeof(chr))
+                if not _.isNaN(chr) 
+                    if chr > max_chr
+                        max_chr = chr
+            return max_chr
+
+
+        get_coordinates: () ->
+            for result in js_data.qtl_results
+                chr = parseInt(result.chr)
+                if _.isNaN(chr)
+                    if result.chr == "X"
+                        chr = @max_chr + 1
+                    else if result.chr == "Y"
+                        chr = @max_chr + 2
         
-    console.log(plot_coordinates)
+                @x_coords.push((chr * 200) + parseFloat(result.Mb))
+                @y_coords.push(result.lrs_value)
+
+
+        create_graph: () ->
+            svg = d3.select("#manhattan_plots")
+                        .append("svg")
+                        .attr("width", 1000)
+                        .attr("height", 800)
         
-    svg = d3.select("#manhattan_plots")
-                .append("svg")
-                .attr("width", 1000)
-                .attr("height", 800)
-                #.attr("transform", "translate(0," + y_max + ")")
-                #.attr("transform", "scale(1,-1)")
-
-
-    svg.selectAll("circle")
-        .data(plot_coordinates)
-        .enter()
-        .append("circle")
-        .attr("cx", (d) =>
-            return (1000 * d[0]/x_max)
-             #return ((900 * (d[0]/x_max)) + 50)
-        )
-        .attr("cy", (d) =>
-             return 800 - (600 * d[1]/y_max)
-        )
-        .attr("r", 3)
\ No newline at end of file
+            svg.selectAll("circle")
+                .data(@plot_coordinates)
+                .enter()
+                .append("circle")
+                .attr("cx", (d) =>
+                    return (1000 * d[0]/@x_max)
+                     #return ((900 * (d[0]/x_max)) + 50)
+                )
+                .attr("cy", (d) =>
+                     return 800 - (600 * d[1]/@y_max)
+                )
+                .attr("r", 3)
+
+    new Manhattan_Plot
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index d231ba5b..d2bc02d7 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -2,49 +2,73 @@
 (function() {
 
   $(function() {
-    var chr, largest_chr, plot_coordinates, result, svg, x_coords, x_max, y_coords, y_max, _i, _j, _len, _len1, _ref, _ref1,
-      _this = this;
-    x_coords = [];
-    y_coords = [];
-    largest_chr = 0;
-    _ref = js_data.qtl_results;
-    for (_i = 0, _len = _ref.length; _i < _len; _i++) {
-      result = _ref[_i];
-      chr = parseInt(result.chr);
-      console.log("foo:", chr, typeof chr);
-      if (_.isNaN(chr)) {
-        console.log("Got NaN");
-      } else {
-        if (chr > largest_chr) {
-          largest_chr = chr;
-        }
+    var Manhattan_Plot;
+    Manhattan_Plot = (function() {
+
+      function Manhattan_Plot() {
+        this.qtl_results = js_data.qtl_results;
+        this.max_chr = this.get_max_chr();
+        this.x_coords = [];
+        this.y_coords = [];
+        this.get_coordinates();
+        this.x_max = d3.max(this.x_coords);
+        this.y_max = d3.max(this.y_coords);
+        this.plot_coordinates = _.zip(this.x_coords, this.y_coords);
+        this.create_graph();
       }
-    }
-    console.log("largest_chr is:", largest_chr);
-    _ref1 = js_data.qtl_results;
-    for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) {
-      result = _ref1[_j];
-      chr = parseInt(result.chr);
-      if (_.isNaN(chr)) {
-        if (result.chr === "X") {
-          chr = largest_chr + 1;
-        } else if (result.chr === "Y") {
-          chr = largest_chr + 2;
+
+      Manhattan_Plot.prototype.get_max_chr = function() {
+        var chr, max_chr, result, _i, _len, _ref;
+        max_chr = 0;
+        _ref = this.qtl_results;
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          result = _ref[_i];
+          chr = parseInt(result.chr);
+          console.log("foo:", chr, typeof chr);
+          if (!_.isNaN(chr)) {
+            if (chr > max_chr) {
+              max_chr = chr;
+            }
+          }
         }
-      }
-      x_coords.push((chr * 200) + parseFloat(result.Mb));
-      y_coords.push(result.lrs_value);
-    }
-    x_max = d3.max(x_coords);
-    y_max = d3.max(y_coords);
-    plot_coordinates = _.zip(x_coords, y_coords);
-    console.log(plot_coordinates);
-    svg = d3.select("#manhattan_plots").append("svg").attr("width", 1000).attr("height", 800);
-    return svg.selectAll("circle").data(plot_coordinates).enter().append("circle").attr("cx", function(d) {
-      return 1000 * d[0] / x_max;
-    }).attr("cy", function(d) {
-      return 800 - (600 * d[1] / y_max);
-    }).attr("r", 3);
+        return max_chr;
+      };
+
+      Manhattan_Plot.prototype.get_coordinates = function() {
+        var chr, result, _i, _len, _ref, _results;
+        _ref = js_data.qtl_results;
+        _results = [];
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          result = _ref[_i];
+          chr = parseInt(result.chr);
+          if (_.isNaN(chr)) {
+            if (result.chr === "X") {
+              chr = this.max_chr + 1;
+            } else if (result.chr === "Y") {
+              chr = this.max_chr + 2;
+            }
+          }
+          this.x_coords.push((chr * 200) + parseFloat(result.Mb));
+          _results.push(this.y_coords.push(result.lrs_value));
+        }
+        return _results;
+      };
+
+      Manhattan_Plot.prototype.create_graph = function() {
+        var svg,
+          _this = this;
+        svg = d3.select("#manhattan_plots").append("svg").attr("width", 1000).attr("height", 800);
+        return svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", function(d) {
+          return 1000 * d[0] / _this.x_max;
+        }).attr("cy", function(d) {
+          return 800 - (600 * d[1] / _this.y_max);
+        }).attr("r", 3);
+      };
+
+      return Manhattan_Plot;
+
+    })();
+    return new Manhattan_Plot;
   });
 
 }).call(this);