Manhattan plot results are appearing correctly for chromosome 1

4 files changed, 81 insertions, 13 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 9bf97f93..5d319006 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -471,7 +471,8 @@ class MarkerRegression(object):
             suggestive_results = []
             self.pure_qtl_results = []
             for result in self.qtl_results:
-                self.pure_qtl_results.append(dict(locus=dict(mb=result.locus.Mb,
+                self.pure_qtl_results.append(dict(locus=dict(name=result.locus.name,
+                                                             mb=result.locus.Mb,
                                                              chromosome=result.locus.chr),
                                                   lrs=result.lrs,
                                                   additive=result.additive))
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index 07a10119..fe7264da 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -41,21 +41,13 @@ $ ->
             #return bars_ordered
     
         display_graph: ->
-            # Figure out the largest key, so we can make sure the x axis max is one larger later on
-            #max_lrs = bars_ordered[bars_ordered.length-1][0]
-            #console.log("max_key is:", max_lrs)
         
             $.jqplot('permutation_histogram',  [@bars_ordered],
                 title: 'Permutation Histogram'     
                 seriesDefaults:
                     renderer:$.jqplot.BarRenderer
                     rendererOptions: 
-                        #barPadding: 30
-                        #barMargin: 30
                         barWidth: 15
-                        #shadowOffset: 2
-                        #shadowDepth: 5
-                        #shadowAlpha: 0.8
                     pointLabels: 
                         show: true
                 axesDefaults:
@@ -63,7 +55,6 @@ $ ->
                 axes: 
                     xaxis: 
                       min: 0
-                      #max: max_lrs + 2
                       label: "LRS"
                       pad: 1.1
                     yaxis:
@@ -81,4 +72,33 @@ $ ->
     #bars_ordered = process_lrs_array()
     #display_permutation_histogram(bars_ordered)
     
-    new Permutation_Histogram
\ No newline at end of file
+    class Manhattan_Plot
+        constructor: ->
+            @process_data()
+            @display_graph()
+            
+        process_data: ->
+            qtl_results = js_data.qtl_results
+            #console.log("qtl_results: ", qtl_results)
+            @plot_points = []
+            for result in qtl_results
+                if result.locus.chromosome == '1'
+                    @plot_points.push([result.locus.mb, result.lrs])
+                
+        display_graph: ->
+            #console.log("@plot_points is:", @plot_points)
+            $.jqplot('manhattan_plot',  [@plot_points],
+                title: '1'     
+                axesDefaults:
+                    labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+                axes: 
+                    xaxis: 
+                      min: 0
+                      label: "Megabases"
+                    yaxis:
+                      min: 0
+                      label: "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 26f0dba4..a9e0024c 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 Permutation_Histogram, sort_number;
+    var Manhattan_Plot, Permutation_Histogram, sort_number;
     sort_number = function(a, b) {
       return a - b;
     };
@@ -72,7 +72,53 @@
       return Permutation_Histogram;
 
     })();
-    return new Permutation_Histogram;
+    Manhattan_Plot = (function() {
+
+      function Manhattan_Plot() {
+        this.process_data();
+        this.display_graph();
+      }
+
+      Manhattan_Plot.prototype.process_data = function() {
+        var qtl_results, result, _i, _len, _results;
+        qtl_results = js_data.qtl_results;
+        this.plot_points = [];
+        _results = [];
+        for (_i = 0, _len = qtl_results.length; _i < _len; _i++) {
+          result = qtl_results[_i];
+          if (result.locus.chromosome === '1') {
+            _results.push(this.plot_points.push([result.locus.mb, result.lrs]));
+          } else {
+            _results.push(void 0);
+          }
+        }
+        return _results;
+      };
+
+      Manhattan_Plot.prototype.display_graph = function() {
+        return $.jqplot('manhattan_plot', [this.plot_points], {
+          title: '1',
+          axesDefaults: {
+            labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+          },
+          axes: {
+            xaxis: {
+              min: 0,
+              label: "Megabases"
+            },
+            yaxis: {
+              min: 0,
+              label: "LRS"
+            }
+          }
+        });
+      };
+
+      return Manhattan_Plot;
+
+    })();
+    new Permutation_Histogram;
+    return new Manhattan_Plot;
   });
 
 }).call(this);
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index 479464ab..ab1cb43b 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -14,6 +14,7 @@
         </div>
     </header>
     
+    <div id="manhattan_plot" style="height:400px;width:900px; "></div>
     <div id="permutation_histogram" style="height:400px;width:900px; "></div>