Checking in before putting the histogram coffeescript into its own

class

3 files changed, 123 insertions, 114 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 52870d84..9bf97f93 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -471,7 +471,7 @@ class MarkerRegression(object):
             suggestive_results = []
             self.pure_qtl_results = []
             for result in self.qtl_results:
-                self.pure_qtl_results.append(dict(locus=dict(cM=result.locus.cM,
+                self.pure_qtl_results.append(dict(locus=dict(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 f3485a82..7ffa0267 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -2,68 +2,76 @@ $ ->
     sort_number = (a, b) ->
         return a - b
 
-    process_lrs_array = ->
-        # Put the data in a format needed for graphing 
-        # The permutation count for a particular integer range (10-11 or 12-13 for example)
-        # will be on the y-axis; LRS values will be on the x-axis
-        lrs_array = js_data.lrs_array
-        bars = {}
-        for lrs in lrs_array
-            floored = Math.floor(lrs)
-            if floored not of bars
-                bars[floored] = 0
-            bars[floored] += 1
 
-        # Now we need to take the unordered hash
-        # And order the keys
-        keys = []
-        for key of bars
-            keys.push(key)
     
-        keys.sort(sort_number)
+        process_lrs_array = ->
+            # Put the data in a format needed for graphing 
+            # The permutation count for a particular integer range (10-11 or 12-13 for example)
+            # will be on the y-axis; LRS values will be on the x-axis
+            lrs_array = js_data.lrs_array
+            bars = {}
+            for lrs in lrs_array
+                floored = Math.floor(lrs)
+                if floored not of bars
+                    bars[floored] = 0
+                bars[floored] += 1
+    
+            # Now we need to take the unordered hash
+            # And order the keys
+            keys = []
+            for key of bars
+                keys.push(key)
         
-
-        # Now that we have the ordered keys above
-        # We can build an array of arrays that jqPlot will use
-        bars_ordered = []
-        for key in keys
-            bars_ordered.push([parseInt(key), bars[key]])
-
-        console.log("bars is:", bars)
-        console.log("keys are:", keys)
-        console.log("bars_ordered are:", bars_ordered)
-        return bars_ordered
-
-    display_permutation_histogram = (bars_ordered) ->
-        # 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)
+            keys.sort(sort_number)
+            
+    
+            # Now that we have the ordered keys above
+            # We can build an array of arrays that jqPlot will use
+            bars_ordered = []
+            for key in keys
+                bars_ordered.push([parseInt(key), bars[key]])
     
-        $.jqplot('permutation_histogram',  [bars_ordered],
-            title: 'Permutation Histogram'     
-            seriesDefaults:
-                renderer:$.jqplot.BarRenderer
-                rendererOptions: 
-                    #barPadding: 30
-                    #barMargin: 30
-                    barWidth: 15
-                    #shadowOffset: 2
-                    #shadowDepth: 5
-                    #shadowAlpha: 0.8
-                pointLabels: 
-                    show: true
-            axesDefaults:
-                labelRenderer: $.jqplot.CanvasAxisLabelRenderer
-            axes: 
-                xaxis: 
-                  min: 0
-                  #max: max_lrs + 2
-                  label: "LRS"
-                  pad: 1.1
-                yaxis:
-                  min: 0
-                  label: "Frequency"
-        )
+            console.log("bars is:", bars)
+            console.log("keys are:", keys)
+            console.log("bars_ordered are:", bars_ordered)
+            return bars_ordered
+    
+        display_permutation_histogram = (bars_ordered) ->
+            # 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:
+                    labelRenderer: $.jqplot.CanvasAxisLabelRenderer
+                axes: 
+                    xaxis: 
+                      min: 0
+                      #max: max_lrs + 2
+                      label: "LRS"
+                      pad: 1.1
+                    yaxis:
+                      min: 0
+                      label: "Frequency"
+            )
+        
+    #process_qtl_results = ->
+    #    qtl_results = js_data.qtl_results
+        
+    #display_manhattan_plot = ->
+
 
 
     bars_ordered = process_lrs_array()
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index ac85dc3d..5d429ddc 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -2,67 +2,68 @@
 (function() {
 
   $(function() {
-    var bars_ordered, display_permutation_histogram, process_lrs_array, sort_number;
+    var bars_ordered, sort_number;
     sort_number = function(a, b) {
+      var display_permutation_histogram, process_lrs_array;
       return a - b;
-    };
-    process_lrs_array = function() {
-      var bars, bars_ordered, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1;
-      lrs_array = js_data.lrs_array;
-      bars = {};
-      for (_i = 0, _len = lrs_array.length; _i < _len; _i++) {
-        lrs = lrs_array[_i];
-        floored = Math.floor(lrs);
-        if (!(floored in bars)) {
-          bars[floored] = 0;
+      process_lrs_array = function() {
+        var bars, bars_ordered, floored, key, keys, lrs, lrs_array, _i, _j, _len, _len1;
+        lrs_array = js_data.lrs_array;
+        bars = {};
+        for (_i = 0, _len = lrs_array.length; _i < _len; _i++) {
+          lrs = lrs_array[_i];
+          floored = Math.floor(lrs);
+          if (!(floored in bars)) {
+            bars[floored] = 0;
+          }
+          bars[floored] += 1;
         }
-        bars[floored] += 1;
-      }
-      keys = [];
-      for (key in bars) {
-        keys.push(key);
-      }
-      keys.sort(sort_number);
-      bars_ordered = [];
-      for (_j = 0, _len1 = keys.length; _j < _len1; _j++) {
-        key = keys[_j];
-        bars_ordered.push([parseInt(key), bars[key]]);
-      }
-      console.log("bars is:", bars);
-      console.log("keys are:", keys);
-      console.log("bars_ordered are:", bars_ordered);
-      return bars_ordered;
-    };
-    display_permutation_histogram = function(bars_ordered) {
-      var max_lrs;
-      max_lrs = bars_ordered[bars_ordered.length - 1][0];
-      console.log("max_key is:", max_lrs);
-      return $.jqplot('permutation_histogram', [bars_ordered], {
-        title: 'Permutation Histogram',
-        seriesDefaults: {
-          renderer: $.jqplot.BarRenderer,
-          rendererOptions: {
-            barWidth: 15
+        keys = [];
+        for (key in bars) {
+          keys.push(key);
+        }
+        keys.sort(sort_number);
+        bars_ordered = [];
+        for (_j = 0, _len1 = keys.length; _j < _len1; _j++) {
+          key = keys[_j];
+          bars_ordered.push([parseInt(key), bars[key]]);
+        }
+        console.log("bars is:", bars);
+        console.log("keys are:", keys);
+        console.log("bars_ordered are:", bars_ordered);
+        return bars_ordered;
+      };
+      return display_permutation_histogram = function(bars_ordered) {
+        var max_lrs;
+        max_lrs = bars_ordered[bars_ordered.length - 1][0];
+        console.log("max_key is:", max_lrs);
+        return $.jqplot('permutation_histogram', [bars_ordered], {
+          title: 'Permutation Histogram',
+          seriesDefaults: {
+            renderer: $.jqplot.BarRenderer,
+            rendererOptions: {
+              barWidth: 15
+            },
+            pointLabels: {
+              show: true
+            }
           },
-          pointLabels: {
-            show: true
-          }
-        },
-        axesDefaults: {
-          labelRenderer: $.jqplot.CanvasAxisLabelRenderer
-        },
-        axes: {
-          xaxis: {
-            min: 0,
-            label: "LRS",
-            pad: 1.1
+          axesDefaults: {
+            labelRenderer: $.jqplot.CanvasAxisLabelRenderer
           },
-          yaxis: {
-            min: 0,
-            label: "Frequency"
+          axes: {
+            xaxis: {
+              min: 0,
+              label: "LRS",
+              pad: 1.1
+            },
+            yaxis: {
+              min: 0,
+              label: "Frequency"
+            }
           }
-        }
-      });
+        });
+      };
     };
     bars_ordered = process_lrs_array();
     return display_permutation_histogram(bars_ordered);