Made Chromosome class in marker_regression.coffee; current

it writes each chromosome's manhattan plot on top of each
other. This commit is before trying to fix that.

2 files changed, 136 insertions, 51 deletions

diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 9f2eb8d7..2f653f98 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -72,28 +72,16 @@ $ ->
     #bars_ordered = process_lrs_array()
     #display_permutation_histogram(bars_ordered)
     
-    class Manhattan_Plot
-        constructor: ->
-            #@chromosomes = {}   # Hash of chromosomes
-            #
-            #@init_chromosomes()
-            
-            @process_data()
-            @display_graph()
+    class Chromosome
+        constructor:  (@name) ->
+            @max_mb = 0
+            @plot_points = []
             
+        process_point: (mb, lrs) ->
+            if mb > @max_mb
+                @max_mb = mb
+            @plot_points.push([mb, lrs])
             
-        process_data: ->
-            qtl_results = js_data.qtl_results
-            #console.log("qtl_results: ", qtl_results)
-            @plot_points = []
-            @max_mb = 0
-            for result in qtl_results
-                if result.locus.chromosome == '1'
-                    mb = parseInt(result.locus.mb)
-                    if mb > @max_mb
-                        @max_mb = mb
-                    @plot_points.push([mb, result.lrs])
-                
         display_graph: ->
             x_axis_max = Math.ceil(@max_mb/25) * 25
             x_axis_ticks = []
@@ -101,11 +89,8 @@ $ ->
             while (x_tick <= x_axis_max)
                 x_axis_ticks.push(x_tick)
                 x_tick += 25
-            console.log("x_axis_ticks:", x_axis_ticks)    
-            console.log("type of x_axis ticks:", typeof(x_axis_ticks[0]), typeof(x_axis_ticks[2]))
-            #console.log("@plot_points is:", @plot_points)
             $.jqplot('manhattan_plot',  [@plot_points],
-                title: '1'
+                title: @name
                 seriesDefaults:
                     showLine: false
                     markerRenderer: $.jqplot.MarkerRenderer
@@ -131,6 +116,68 @@ $ ->
                         tickOptions:
                             showGridline: false
             )
+            
+        
+            
+        
+    
+    class Manhattan_Plot
+        constructor: ->
+            @chromosomes = {}   # Hash of chromosomes
+            
+            @build_chromosomes()
+            
+            #@process_data()
+            @display_graphs()
+            
+        build_chromosomes: ->
+            for result in js_data.qtl_results
+                #if result.locus.chromosome == '1'
+                chromosome = result.locus.chromosome
+                if chromosome not of @chromosomes
+                    @chromosomes[chromosome] = new Chromosome(chromosome)
+                mb = parseInt(result.locus.mb)
+                @chromosomes[chromosome].process_point(mb, result.lrs)
+                 
+                    #if mb > @max_mb
+                    #    @max_mb = mb
+                    #@plot_points.push([mb, result.lrs])                    
+        
+        display_graphs: ->
+            ### Call display_graph for each chromosome ###
+            
+            # First get everything in the right order
+            numbered_keys = []
+            extra_keys = []
+            for key of @chromosomes
+                if isNaN(key)
+                    extra_keys.push(key)
+                else
+                    numbered_keys.push(key)
+        
+            numbered_keys.sort(sort_number)
+            extra_keys.sort()
+            keys = numbered_keys + extra_keys
+            console.log("keys are:", keys)
+            
+            for chromosome in key
+                @chromosomes[chromosome].display_graph()
+            
+            
+            
+        #process_data: ->
+        #    qtl_results = js_data.qtl_results
+        #    #console.log("qtl_results: ", qtl_results)
+        #    @plot_points = []
+        #    @max_mb = 0
+        #    for result in qtl_results
+        #        if result.locus.chromosome == '1'
+        #            mb = parseInt(result.locus.mb)
+        #            if mb > @max_mb
+        #                @max_mb = mb
+        #            @plot_points.push([mb, result.lrs])
+                
+
 
     new Permutation_Histogram
     new Manhattan_Plot
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index c69d0340..7553721c 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -2,7 +2,7 @@
 (function() {
 
   $(function() {
-    var Manhattan_Plot, Permutation_Histogram, sort_number;
+    var Chromosome, Manhattan_Plot, Permutation_Histogram, sort_number;
     sort_number = function(a, b) {
       return a - b;
     };
@@ -72,35 +72,22 @@
       return Permutation_Histogram;
 
     })();
-    Manhattan_Plot = (function() {
+    Chromosome = (function() {
 
-      function Manhattan_Plot() {
-        this.process_data();
-        this.display_graph();
+      function Chromosome(name) {
+        this.name = name;
+        this.max_mb = 0;
+        this.plot_points = [];
       }
 
-      Manhattan_Plot.prototype.process_data = function() {
-        var mb, qtl_results, result, _i, _len, _results;
-        qtl_results = js_data.qtl_results;
-        this.plot_points = [];
-        this.max_mb = 0;
-        _results = [];
-        for (_i = 0, _len = qtl_results.length; _i < _len; _i++) {
-          result = qtl_results[_i];
-          if (result.locus.chromosome === '1') {
-            mb = parseInt(result.locus.mb);
-            if (mb > this.max_mb) {
-              this.max_mb = mb;
-            }
-            _results.push(this.plot_points.push([mb, result.lrs]));
-          } else {
-            _results.push(void 0);
-          }
+      Chromosome.prototype.process_point = function(mb, lrs) {
+        if (mb > this.max_mb) {
+          this.max_mb = mb;
         }
-        return _results;
+        return this.plot_points.push([mb, lrs]);
       };
 
-      Manhattan_Plot.prototype.display_graph = function() {
+      Chromosome.prototype.display_graph = function() {
         var x_axis_max, x_axis_ticks, x_tick;
         x_axis_max = Math.ceil(this.max_mb / 25) * 25;
         x_axis_ticks = [];
@@ -109,10 +96,8 @@
           x_axis_ticks.push(x_tick);
           x_tick += 25;
         }
-        console.log("x_axis_ticks:", x_axis_ticks);
-        console.log("type of x_axis ticks:", typeof x_axis_ticks[0], typeof x_axis_ticks[2]);
         return $.jqplot('manhattan_plot', [this.plot_points], {
-          title: '1',
+          title: this.name,
           seriesDefaults: {
             showLine: false,
             markerRenderer: $.jqplot.MarkerRenderer,
@@ -148,6 +133,59 @@
         });
       };
 
+      return Chromosome;
+
+    })();
+    Manhattan_Plot = (function() {
+
+      function Manhattan_Plot() {
+        this.chromosomes = {};
+        this.build_chromosomes();
+        this.display_graphs();
+      }
+
+      Manhattan_Plot.prototype.build_chromosomes = function() {
+        var chromosome, mb, result, _i, _len, _ref, _results;
+        _ref = js_data.qtl_results;
+        _results = [];
+        for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+          result = _ref[_i];
+          chromosome = result.locus.chromosome;
+          if (!(chromosome in this.chromosomes)) {
+            this.chromosomes[chromosome] = new Chromosome(chromosome);
+          }
+          mb = parseInt(result.locus.mb);
+          _results.push(this.chromosomes[chromosome].process_point(mb, result.lrs));
+        }
+        return _results;
+      };
+
+      Manhattan_Plot.prototype.display_graphs = function() {
+        /* Call display_graph for each chromosome
+        */
+
+        var chromosome, extra_keys, key, keys, numbered_keys, _i, _len, _results;
+        numbered_keys = [];
+        extra_keys = [];
+        for (key in this.chromosomes) {
+          if (isNaN(key)) {
+            extra_keys.push(key);
+          } else {
+            numbered_keys.push(key);
+          }
+        }
+        numbered_keys.sort(sort_number);
+        extra_keys.sort();
+        keys = numbered_keys + extra_keys;
+        console.log("keys are:", keys);
+        _results = [];
+        for (_i = 0, _len = key.length; _i < _len; _i++) {
+          chromosome = key[_i];
+          _results.push(this.chromosomes[chromosome].display_graph());
+        }
+        return _results;
+      };
+
       return Manhattan_Plot;
 
     })();