Worked with the manhattan plot coffeescript to set x-axis and change

the plot point sizes and remove lines

4 files changed, 63 insertions, 8 deletions

diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.coffee b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
index fe7264da..cb19712f 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.coffee
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.coffee
@@ -81,23 +81,46 @@ $ ->
             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'
+                    if parseInt(result.locus.mb) > @max_mb
+                        @max_mb = result.locus.mb
                     @plot_points.push([result.locus.mb, result.lrs])
                 
         display_graph: ->
+            x_axis_max = Math.ceil(@max_mb/25) * 25
+            x_axis_ticks = []
+            x_tick = 0
+            while (x_tick <= x_axis_max)
+                x_axis_ticks.push(x_tick)
+                x_tick += 25
             #console.log("@plot_points is:", @plot_points)
             $.jqplot('manhattan_plot',  [@plot_points],
-                title: '1'     
+                title: '1'
+                seriesDefaults:
+                    showLine: false
+                    markerRenderer: $.jqplot.MarkerRenderer
+                    markerOptions:
+                        style: "filledCircle"
+                        size: 3                   
                 axesDefaults:
+                    tickRenderer: $.jqplot.CanvasAxisTickRenderer
                     labelRenderer: $.jqplot.CanvasAxisLabelRenderer
                 axes: 
                     xaxis: 
-                      min: 0
-                      label: "Megabases"
+                        min: 0
+                        max: x_axis_max
+                        ticks: x_axis_ticks
+                        tickOptions:
+                            angle: 90
+                            showGridline: false
+                        label: "Megabases"
                     yaxis:
-                      min: 0
-                      label: "LRS"
+                        min: 0
+                        label: "LRS"
+                        tickOptions:
+                            showGridline: false
             )
 
     new Permutation_Histogram
diff --git a/wqflask/wqflask/static/new/javascript/marker_regression.js b/wqflask/wqflask/static/new/javascript/marker_regression.js
index a9e0024c..30e287dd 100644
--- a/wqflask/wqflask/static/new/javascript/marker_regression.js
+++ b/wqflask/wqflask/static/new/javascript/marker_regression.js
@@ -83,10 +83,14 @@
         var 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') {
+            if (parseInt(result.locus.mb) > this.max_mb) {
+              this.max_mb = result.locus.mb;
+            }
             _results.push(this.plot_points.push([result.locus.mb, result.lrs]));
           } else {
             _results.push(void 0);
@@ -96,19 +100,45 @@
       };
 
       Manhattan_Plot.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 = [];
+        x_tick = 0;
+        while (x_tick <= x_axis_max) {
+          x_axis_ticks.push(x_tick);
+          x_tick += 25;
+        }
         return $.jqplot('manhattan_plot', [this.plot_points], {
           title: '1',
+          seriesDefaults: {
+            showLine: false,
+            markerRenderer: $.jqplot.MarkerRenderer,
+            markerOptions: {
+              style: "filledCircle",
+              size: 3
+            }
+          },
           axesDefaults: {
+            tickRenderer: $.jqplot.CanvasAxisTickRenderer,
             labelRenderer: $.jqplot.CanvasAxisLabelRenderer
           },
           axes: {
             xaxis: {
               min: 0,
+              max: x_axis_max,
+              ticks: x_axis_ticks,
+              tickOptions: {
+                angle: 90,
+                showGridline: false
+              },
               label: "Megabases"
             },
             yaxis: {
               min: 0,
-              label: "LRS"
+              label: "LRS",
+              tickOptions: {
+                showGridline: false
+              }
             }
           }
         });
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index ab1cb43b..68effbd5 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -14,7 +14,7 @@
         </div>
     </header>
     
-    <div id="manhattan_plot" style="height:400px;width:900px; "></div>
+    <div id="manhattan_plot" style="height:400px;width:150px; "></div>
     <div id="permutation_histogram" style="height:400px;width:900px; "></div>
 
 
@@ -32,7 +32,9 @@
     <![endif]-->
     <script language="javascript" type="text/javascript" src="/static/packages/jqplot/jquery.jqplot.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/jqplot/plugins/jqplot.pointLabels.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/jqplot/plugins/jqplot.canvasAxisTickRenderer.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/jqplot/plugins/jqplot.barRenderer.min.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/jqplot/plugins/jqplot.markerRenderer.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/jqplot/plugins/jqplot.canvasTextRenderer.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/jqplot/plugins/jqplot.canvasAxisLabelRenderer.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/javascript/marker_regression.js"></script>
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index 15e2efe9..84196959 100644
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -30,7 +30,7 @@
                     <div class="control-group">
                         <label for="mapping_permutations" class="control-label">Permutations (n)</label>
                         <div class="controls">
-                            <input name="num_perm" value="2000" type="text" />
+                            <input name="num_perm1" value="2000" type="text" />
                         </div>
                     </div>